Sequence-specific inhibition of small RNA function

ABSTRACT

The present invention relates to the discovery of a method for inhibiting RNA silencing in a target sequence-specific manner. RNA silencing requires a set of conserved cellular factors to suppress expression of gene-encoded polypeptide. The invention provides compositions for sequence-specific inactivation of the RISC component of the RNA silencing pathway, and methods of use thereof. The RISC inactivators of the present invention enable a variety of methods for identifying and characterizing miRNAs and siRNAs, RISC-associated factors, and agents capable of modulating RNA silencing. Therapeutic methods and compositions incorporating RISC inactivators and therapeutic agents identified through use of RISC inactivators are also featured.

RELATED APPLICATIONS

This application claims the benefit of U.S. Ser. No. 60/543,796,entitled “Sequence-Specific Inhibition of Small RNA Function,” filed onFeb. 10, 2004, and U.S. Ser. No. 60/525,474, entitled “Sequence-SpecificInhibition of Small RNA Function,” filed on Nov. 26, 2003. The entirecontents of these applications are hereby incorporated herein byreference.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

Funding for the work described herein was at least in part provided bythe federal government (N.I.H. grants GM62862-01 and GM65236-01, andGM58800).

BACKGROUND OF THE INVENTION

The endoribonuclease Dicer produces two types of small regulatory RNAsthat regulate gene expression: small interfering RNAs (siRNAs) andmicroRNAs (miRNAs) (Bernstein et al., 2001; Grishok et al., 2001;Hutvágner et al., 2001; Ketting et al., 2001; Knight and Bass, 2001). Inanimals, siRNAs direct target mRNA cleavage (Elbashir et al., 2001c;Elbashir et al., 2001d), whereas miRNAs block target mRNA translation(Lee et al., 1993; Reinhart et al., 2000; Brennecke et al., 2003; Xu etal., 2003). Recent data suggest that both siRNAs and miRNAs incorporateinto similar perhaps even identical protein complexes, and that acritical determinant of mRNA destruction versus translation regulationis the degree of sequence complementary between the small RNA and itsmRNA target (Hutvágner and Zamore, 2002; Mourelatos et al., 2002; Zenget al., 2002; Doench et al., 2003; Saxena et al., 2003; Zeng et al.,2003a).

Target RNA cleavage directed by siRNA is called RNA interference (RNAi).RNAi is a powerful method for the study of gene function in animals andplants and is being developed as a therapy for treating geneticdisorders and viral infections. Biochemical studies in Drosophila S2cells (Bernstein et al., 2001; Hammond et al., 2001 a; Caudy et al.,2002; Liu et al., 2003) and affinity purification (Martinez et al.,2002) or immunoprecipitation (Hutvágner and Zamore, 2002) from culturedhuman HeLa cells have identified protein components of the RNAi effectorcomplex, the RNA-induced silencing complex (RISC; the RISC complex alsofunctions in miRNA-mediated translational silencing). Genetic mutationsthat disrupt RNAi in C. elegans, Drosophila, green algae, fungi andplants have likewise identified proteins required for RNAi (Cogoni andMacino, 1997; Cogoni and Macino, 1999a; Cogoni and Macino, 1999b;Ketting et al., 1999; Tabara et al., 1999; Catalanotto et al., 2000;Dalmay et al., 2000; Fagard et al., 2000; Grishok et al., 2000; Kettingand Plasterk, 2000; Mourrain et al., 2000; Wu-Scharf et al., 2000;Dalmay et al., 2001; Catalanotto et al., 2002; Grishok and Mello, 2002;Tabara et al., 2002; Tijsterman et al., 2002a; Tijsterman et al.,2002b). Key steps in the RNAi pathway have also emerged from studies ofRNAi reconstituted in cell-free extracts (Tuschl et al., 1999; Zamore etal., 2000; Hammond et al., 2001b; Nykänen et al., 2001; Martinez et al.,2002; Schwarz et al., 2002; Tang et al., 2003).

Recently hundreds of miRNAs have been identified in animals and plants(Lagos-Quintana et al., 2001; Lau et al., 2001; Lee and Ambros, 2001;Lagos-Quintana et al., 2002; Reinhart et al., 2002; Ambros et al., 2003;Aravin et al., 2003; Brennecke and Cohen, 2003; Lim et al., 2003). Ofthese, the biological functions of at least four animal miRNAs areknown. In C. elegans, the miRNAs lin-4 (Locus link ID 266860; Lee etal., 1993; Olsen and Ambros, 1999) and let-7 (Locus link ID 266954;Reinhart et al., 2000) regulate developmental timing, whereas theDrosophila miRNAs bantam (Locus link ID 117376) and miR-14 (Locus linkID 170868) control cell survival by repressing translation ofpro-apoptotic genes (Brennecke et al., 2003; Xu et al., 2003).Computational approaches have also been described to assist inidentifying the mRNA targets of other miRNAs (Enright et al., 2003;Lewis et al., 2003; Stark et al., 2003). Despite the widespread use ofRNAi to ‘knock down’ gene function and the increasing body of evidencesupporting a role for miRNAs in RNA silencing, the mechanisms by whichthese processes occur are not yet fully understood. Accordingly, thereexists a need for a more complete understanding of the mechanismsunderlying RNA silencing (e.g., RNAi, miRNA-mediated translationalsilencing), as well as for compounds which can regulate RNA silencing.

SUMMARY OF THE INVENTION

The present invention is based, at least in part, on the discovery thatRISC inactivators are potent and irreversible inhibitors of smallRNA-directed RNA silencing in vivo and in vitro. In particular, theinvention is based, at least in part, on the discovery that 2′-O-methyloligonucleotides are potent and irreversible inhibitors of smallRNA-directed RNA silencing in vivo and in vitro. Accordingly, thepresent invention relates to methods of modulating (e.g., inhibiting)RNA silencing, in particular, microRNA (miRNA)-mediated and/orsiRNA-mediated RNA silencing. The RNA silencing-inhibitory agents of theinvention are suitable for use in modulating RNA silencing both in vitroand in vivo. In vivo methodologies are useful for both general RNAsilencing modulatory purposes as well as in therapeutic applications inwhich RNA silencing modulation (e.g., inhibition) is desirable. Use ofRNA silencing is of use in investigation of disease states, e.g.,oncogenesis and infectious disease. Insulin secretion has recently beenshown to be regulated by at least one miRNA (Poy et al. 2004), and arole for miRNAs has also been implicated in spinal muscular atrophy(SMA; Mourelatos et al. 2002). There is therefore mounting evidence thatthe activities of siRNAs and miRNAs could impact a broad range ofdisease states.

The present invention provides compositions for sequence-specific RISCinactivation and methods of use thereof. In particular, the inventionprovides RISC inactivators (e.g., 2′-O-methyl oligonucleotides, as wellas similarly effective RISC inactivators, e.g., locked nucleic acid(LNA) and phosphorothidate-modified oligonucleotides) for modulating RNAsilencing in a sequence-specific manner in vitro and in vivo. Methodsfor using RISC inactivators are also provided, including:

-   -   methods for identifying agents capable of modulating RNA        silencing    -   methods for identifying RISC-associated factors.    -   methods for identifying and characterizing functions of miRNAs        and siRNAs.    -   methods for monitoring inhibition of RNA silencing.    -   methods for measuring levels of programmed RISC.

Therapeutic methods and compositions incorporating RISC inactivators andtherapeutic agents identified through use of RISC inactivators are alsofeatured.

Other features and advantages of the invention will be apparent from thefollowing detailed description and claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows that a 2′-O-methyl RNA oligonucleotide inhibited RNAi invitro in Drosophila embryo lysate. FIG. 1A depicts sequences of thesense and anti-sense Pp-luc target RNAs (black), the siRNA (red,anti-sense strand; black, sense strand), and the sense and anti-sense2′-O-methyl oligonucleotides (blue) used. FIG. 1B showssequence-specific depletion of RNAi activity by immobilized 2′-O-methyloligonucleotides from Drosophila embryo lysate programmed with siRNA.siRNA was incubated with lysate to assemble RISC, then immobilized2′-O-methyl oligonucleotide was added. Beads were then removed from thesupernatant, and either sense or anti-sense ³²P-radiolabeled target RNAwas added to the supernatant to measure RISC activity for each siRNAstrand. Ø, target RNA before incubation with siRNA-programmed lysate; T,total reaction before depletion; unbound, the supernatant afterincubation with the immobilized anti-sense (AS) or sense (S) 2′-O-methyloligonucleotides shown in FIG. 1A. The absence of 5′ cleavage productdemonstrated that the sense oligonucleotide depleted RISC containinganti-sense siRNA, but not sense siRNA, and the anti-senseoligonucleotide depleted the sense RISC, but not that containinganti-sense siRNA. Bi, 5′ biotin attached via a six-carbon linker.

FIG. 2 shows that 2′-O-methyl oligonucleotides acted as stoichiometric,irreversible inhibitors of RISC function. FIG. 2A depicts results ofusing the immobilized sense 2′-O-methyl oligonucleotide to determine theconcentration of ³²P-radiolabeled anti-sense siRNA assembled into RISCin Drosophila embryo. The 2′-O-methyl oligonucleotide and siRNA duplexare shown in FIG. 1A. FIG. 2B-2G graphically depict measurement ofinhibition of RNAi using free 2′-O-methyl oligonucleotide and 1.3 nM(2B), 4.6 nM (2C), 9.3 nM (2D), 14.5 nM (2E), 18 nM (2F), 23.5 nM (2G)RISC. The concentration of 2′-O-methyl oligonucleotide required forhalf-maximal inhibition (IC50) was calculated by fitting each data setto a sigmoidal curve using a Hill coefficient of one. FIG. 2H depicts aplot of IC50 versus RISC concentration, which indicated that each2′-O-methyl oligonucleotide bound a single RISC. These data alsoindicated that binding was essentially irreversible.

FIG. 3 shows that RISC did not act through an anti-sense mechanism. FIG.3A shows that inhibition of sense-target cleavage by an anti-sense2′-O-methyl oligonucleotide required ˜40-fold higher concentration thanby a sense oligonucleotide. The anti-sense oligonucleotide could paircompletely with the sense target RNA, but not with the anti-sensesiRNA-programmed RISC. The IC50 value and the RISC concentration areindicated. Also shown are the sequences of the sense Pp-luc RNA target(black), the siRNA (red, anti-sense strand; black, sense strand), andthe 2′-O-methyl oligonucleotide (blue). FIG. 3B shows that the sameantisense 2′-O-methyl oligonucleotide was an effective competitor ofanti-sense target cleavage. In this experiment, inhibition occurred viabinding of the anti-sense oligonucleotide to the sense siRNA-programmedRISC, not the target RNA. The IC50 value and the RISC concentration areindicated. Also shown are the sequences of the Pp-luc anti-sense RNAtarget (black), the siRNA (red, anti-sense strand; black, sense strand)and the 2′-O-methyl oligonucleotide (blue). The G:U wobble in the siRNAduplex in (B) acts to direct the sense-strand into RISC and improve itsefficacy in target cleavage.

FIG. 4 shows that a 2′-O-methyl oligonucleotide was a potent inhibitorof RNAi in human cultured HeLa cells. In FIG. 4A-4D, HeLa cells weretransfected with 1 nM (4A), 5 nM (4B), 10 nM (4C), or 25 nM (4D) siRNAtargeting Pp-luc mRNA. The next day the cells were cotransfected withRr-luc and Pp-luc expressing plasmids together with various amounts of a31-nucleotide 2′-O-methyl oligonucleotide complementary to theanti-sense strand of the siRNA. The half-maximal concentration of2′-O-methyl oligonucleotide required to inhibit (IC50) was determined byfitting the data to a sigmoidal curve using a Hill coefficient of one.FIG. 4E depicts IC50 plotted as a function of the concentration oftransfected siRNA.

FIG. 5 depicts that a complementary 2′-O-methyl oligonucleotide blockedendogenous let7-containing RISC function. FIG. 5A shows the sequence ofthe let-7 complementary site in the target RNA (black), of the siRNA(red, anti-sense strand; black, sense strand) and of thelet-7-complementary 2′-O-methyl oligonucleotide (blue). FIG. 5B depictsa schematic representation of the target RNA, which contained bothPp-luc and anti-sense let-7 sequences. The left lanes of FIG. 5C showthe result of an experiment in which Drosophila embryo lysate wasprogrammed with let-7 siRNA, then the target RNA and the 2′-O-methyloligonucleotide were added together. The right lanes of FIG. 5C show theresult obtained by adding target RNA and 2′-O-methyl oligonucleotide toHeLa S100 extract, which contains endogenous human let-7-programmedRISC. FIG. 5D shows that an RNA target containing both Pp-luc andanti-sense let-7 sequence could be simultaneously targeted by Pp-lucsiRNA and endogenous let-7 in HeLa S100 lysate. The let-7-complementary2′-O-methyl oligonucleotide blocked let-7-, but not Pp-luc siRNA-,programmed RISC function. The lower panel shows the same samplesanalyzed separately to resolve better the let-7 5′ cleavage product. InFIG. SE, Drosophila embryo lysate was programmed with let-7 siRNA andthen incubated with biotinylated 2′-O-methyl oligonucleotide tethered toparamagnetic streptavidin beads. The beads were removed and thesupernatant tested for RNAi activity. Ø, target RNA before incubationwith siRNA-programmed lysate; T, total reaction before depletion;unbound, the supernatant after incubation with the paramagnetic beads.‘Mock’ indicates no oligonucleotide was used on the beads; ‘let-7’indicates that the beads contained the let-7-complementaryoligonucleotide shown in FIG. 5A.

FIG. 6 shows that injection of a 2′-O-methyl oligonucleotidecomplementary to let-7 miRNA could phenocopy the loss of let-7 functionin C. elegans. In FIG. 6A, wild-type and lin-41(ma104) L2 stage C.elegans larvae were injected with either a 2′-O-methyl oligonucleotidecomplementary to let-7 miRNA (FIG. 5A) or an unrelated Pp-luc2′-O-methyl oligonucleotide. Absence of alae and presence of burstingvulvae were scored when the injected animals reached adulthood. FIG. 6Bdepicts isolation of let-7-associated proteins with a tethered2′-O-methyl oligonucleotide. Northern analysis of let-7 miRNA remainingin the supernatant of the worm lysate after incubation with thelet-7-complementary (let-7) or Pp-luc (unrelated) oligonucleotide isshown. Input represented the equivalent of 50% of the total extractincubated with tethered oligonucleotide. FIG. 6C depicts Western blotanalysis of the GFP-tagged ALG-1 and ALG-2 proteins associated withlet-7. Extracts from a transgenic strain expressing the tagged proteinswere incubated with the indicated tethered 2′-O-methyl oligonucleotide,then the beads were washed and bound proteins fractionated on an 8%polyacrylamide/SDS gel. Western blots were probed using anti-GFPmonoclonal or anti-RDE4 polyclonal antibody. The RDE4-specific band ismarked with an asterisk (Tabara et al., 2002). FIG. 6D depicts Northernanalysis of let-7 miRNA in ALG-1/ALG-2 complexes. Extracts prepared frommixed stage wild-type worms (N2), or GFP::ALG-1/ALG-2 transgenic worms,were immunoprecipitated using anti-GFP monoclonal antibodies. Theunbound and immunoprecipitated RNAs were analyzed by Northernhybridization for let-7 and, in FIG. 6E, 5% of the immunoprecipitatedprotein was analyzed by Western blotting for GFP to confirm recovery ofthe GFP-tagged ALG1/2 proteins.

FIG. 7 depicts that let-7 is developmentally regulated in NT2 cells.FIG. 7A shows by Northern blot that the let-7 gene family was expressedin HeLa cells and differentiated NT2N cells but not in undifferentiatedNT2 cells. FIG. 7B shows that the activity of a Luciferase reporterplasmid containing let-7 responsive element (LRE) was repressed in thelet-7 expressing cell lines. (MLRE was a control Luciferase genecontaining scrambled let-7 responsive element that was not sensitive tolet-7-mediated repression.) FIG. 7C depicts that 2′-O-methyloligonucleotides were potent inhibitors of let-7 in HeLa cells. FIG. 7Dshows that exogenous let-7 regulated the expression of the LREcontaining reporter gene.

FIG. 8 shows that let-7 altered the RNA levels of its target genes. FIG.8A shows putative let-7 target genes, for which expression wassignificantly altered upon let-7 inhibiton in HeLa cells and let-7over-expression in NT2 cells. FIG. 8B depicts results of real-time PCRanalysis of EMGA2and Dicer transcripts in HeLa cells upon inhibition oflet-7 with a 2′-O-methyl oligonucleotide FIG. 8C shows the results ofreal-time PCR analysis of HMGA2 and Dicer transcripts in NT2 cells upontransfection of let-7 siRNA.

FIG. 9 shows that expressed levels of HMGA2 and Dicer proteins werelet-7 dependent. FIG. 9A demonstrates that Dicer expression wasincreased in HeLa cells upon let-7 inhibition, with relative Dicerprotein levels indicated. FIG. 9B shows that HMGA2 protein expressionwas developmentally regulated in NT2 cells. Different human cell linesand mouse NIH3T3 cells were tested for HMGA2 expression, with relativelevels of HMG2A expression indicated. HMGA2 expression was dramaticallydecreased in NT2N cells upon retinoic acid induced differentiation ofNT2 cells. FIG. 9C depicts that let-7 repressed HMGA2 expression in NT2cells. Cells were transfected with let-7 siRNA and two siRNAs thattarget the HMGA2 mRNA, with relative levels of HMGA2 protein indicated.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to the discovery of a method by which toselectively inhibit RNA silencing in a targeted, sequence-specificmanner. The invention therefore features RISC inactivators (e.g.,2′-O-methyl oligonucleotides, and one of skill in the art will recognizethat effective RISC inactivators may also be synthesized usingoligonucleotides containing, e.g., locked nucleic acids (LNA),phosphorothioate modifications, or other equivalents). A form of RISCinactivator, specifically a 2′-O-methyl oligonucleotide, was identifiedas being capable of potently and irreversibly inhibiting smallRNA-directed RNA silencing in vivo and in vitro. A 2′-O-methyloligonucleotide complementary to an siRNA was shown to be capable ofblocking mRNA cleavage in Drosophila embryo lysates and HeLa cell S100extracts and in cultured human HeLa cells. In Caenorhabditis elegans,injection of the 2′-O-methyl oligonucleotide complementary to the miRNAlet-7 induced a let-7 loss-of-function phenocopy. Using an immobilized2′-O-methyl oligonucleotide, it was demonstrated that the C. elegansArgonaute proteins ALG-1 and ALG-2, which were previously implicated inlet-7 function through genetic studies, were constituents of alet-7-containing protein-RNA complex. Thus, it was shown that2′-O-methyl RNA oligonucleotides provide an efficient andstraightforward way to block small RNA function in vivo and furthermoreare useful for identifying small RNA-associated proteins that mediateRNA silencing pathways.

These experiments using 2′-O-methyl oligonucleotides also demonstratedthat the acquisition of a target RNA by an siRNA-programmed RISC was farmore efficient than the binding of an anti-sense oligonucleotide to thesame region of the target. To demonstrate the utility of 2′-O-methyloligonucleotides in probing RNA silencing pathways, it was shown that2′-O-methyl oligonucleotides efficiently blocked siRNA-directed RISCactivity in cell extracts and in cultured human HeLa cells. Wheninjected into Caenorhabditis elegans larvae, a let-7-complementary2′-O-methyl oligonucleotide could efficiently suppress lin-41translational repression by the let-7 miRNA. Finally, a tethered2′-O-methyl oligonucleotide was used to demonstrate association of theC. elegans Argonaute proteins ALG-1 and ALG-2 with let-7.

The methods of the present invention enable the extensivecharacterization of naturally-occurring microRNAs (miRNAs) and siRNAs.Hundreds of microRNAs (miRNAs) and endogenous small interfering RNAs(siRNAs) have been identified from both plants and animals, yet with fewexceptions, little is known about their biochemical modes of action andeven about their biological functions. The discovery of the inventionthat RISC-inactivating agents, specifically 2′-O-methyloligonucleotides, effectively inhibit RNA silencing (e.g., RNAi,miRNA-mediated translational silencing) in a sequence-specific mannerdirectly facilitates extensive characterization of both miRNAs andsiRNAs. In addition, the methods of the present invention also enablemethods for identifying therapeutic compounds capable of modulating RNAsilencing activity.

RISC inactivators of the invention are of any size and/or chemicalcomposition sufficient to inhibit RNA silencing, in particular, microRNA(miRNA)-mediated and/or siRNA-mediated RNA silencing. In exemplaryembodiments, the RISC inactivators are oligonucleotides of between about10-100 nucleotides (or modified nucleotides), preferably between about10-40 nucleotides (or modified nucleotides) (e.g., ribonucleotides ormodified ribonucleotides), for example, between about 15-35, e.g., about15-20, 20-25, 25-30 or 30-35 (31, 32, 33, 34, 35) 40 nucleotides (ormodified nucleotides) (e.g., ribonucleotides or modifiedribonucleotides).

RNA silencing-inhibitory agents (RISC inactivators) are preferablysufficiently complementary to miRNA sequences or to siRNA sequences, inparticular, the guide strand or antisense strand sequences of an siRNA.

The invention-further relates to methods for identifyingmiRNA-associating agents, for example, agents or compounds associatedwith miRNAs in vivo. In particular, the invention provides methods forisolating, identifying and/or characterizing constituents ofmiRNA-containing complexes, e.g., miRNA-containing protein-RNAcomplexes. Such constituents (e.g., miRNA-associated proteins) can bethemselves used as modulators of RNA silencing pathways or can be usedin further assays (e.g., screening assays) to identify compoundssuitable for modulating such pathways.

In a preferred embodiment, the invention includes a method forinhibiting the RNA silencing of individual genes, through use of a RISCinactivator that is designed to anneal to the guide strand of an siRNAor miRNA, with said siRNA or miRNA normally functioning to direct RNAsilencing of a specific target gene. In one embodiment, a cellcontaining an siRNA or miRNA that directs RNA silencing of a gene iscontacted by a RISC inactivator sufficiently complementary to the guidestrand of the siRNA or miRNA to achieve inhibition of the RNA silencingactivity of the specific siRNA or miRNA to which the RISC inactivator istargeted. In a related embodiment, an organism is contacted by a RISCinactivator to achieve such gene-specific inhibition of RNA silencing.

In another embodiment, the RISC inactivators (RISC inhibitors) of theinvention are utilized to identify factors that associate with siRNA ormiRNA molecules. Specifically, a cell containing an siRNA or miRNA thatdirects RNA silencing of a specific gene is contacted with a RISCinactivator sufficiently complementary to the siRNA or miRNA to induceinhibition of the RNA silencing of a target gene normally directed bythe siRNA or miRNA. Because the RISC inactivator anneals in a stable andspecific manner to the siRNA or miRNA in the presence of RISC andassociated factors, enrichment for the RISC inactivator or targetedsiRNA or miRNA also enriches for RISC and other associated factors, thusallowing for identification of siRNA- or miRNA-associated factors.

In an additional embodiment, the RISC inactivator (RISC inhibitor) ofthe invention is nuclease-resistant.

In a further embodiment, the RISC inactivator (RISC inhibitor) of theinvention is ribonuclease-resistant.

In a-related embodiment, the RISC inactivator (RISC inhibitor) of theinvention is a 2′-O-methyl oligonucleotide.

In a further embodiment, the RISC inactivator of the invention comprisesan oligonucleotide containing at least one locked nucleic acid (LNA).

In an additional embodiment, the RISC inactivator of the inventioncomprises an oligonucleotide containing at least one phosphorothioatemodification.

In another embodiment, the RISC inactivator (RISC inhibitor) of theinvention is modified with a moiety selected from the group consistingof the 2′-OH group replaced by a H, alkoxy or OR, halogen, SH, SR, amino(such as NH2, NHR, NR2,), or CN group, wherein R is lower alkyl,alkenyl, alkynyl, or aryl.

In an additional embodiment, the cell or organism of the invention is aDrosophila melanogaster cell or organism; and a further embodimentspecifies the Drosophila melanogaster cell or organism to be aDrosophila melanogaster embryo.

In another embodiment, the cell or organism of the invention is aCaenorhabditis elegans cell or organism.

In a further embodiment, the cell or organism of the invention is amammalian cell or organism.

In another embodiment, the RISC inactivators of the invention areutilized to identify factors within a composition that associate withmiRNA molecules. Specifically, a composition containing a miRNA thatdirects RNA silencing of a specific gene is contacted with a RISCinactivator sufficiently complementary to the miRNA to induce inhibitionof the RNA silencing of a target gene normally directed by the miRNA.Because the RISC inactivator anneals in a stable and specific manner tothe miRNA in the presence of RISC and associated factors, enrichment forthe RISC inactivator or targeted miRNA also enriches for RISC and otherassociated factors, thus allowing for identification of miRNA-associatedfactors.

In a related embodiment, factors within a composition that associatewith siRNA molecules are identified by the invention in the same manneras the method used to identify siRNA-associated factors. Specifically, acomposition containing an siRNA that directs RNA silencing of a specificgene is contacted with a RISC inactivator sufficiently complementary tothe siRNA to induce inhibition of the RNA silencing of a target genenormally directed by the siRNA. Because the RISC inactivator anneals ina stable and specific manner to the siRNA in the presence of RISC andassociated factors, enrichment-for the RISC inactivator or targetedsiRNA also enriches for RISC and other associated factors, thus allowingfor identification of siRNA-associated factors.

In an additional embodiment, the RISC inactivator (RISC inhibitor) ofthe invention is nuclease-resistant.

In a further embodiment, the RISC inactivator (RISC inhibitor) of theinvention is ribonuclease-resistant.

In a related embodiment, the RISC inactivator (RISC inhibitor) of theinvention is a 2′-O-methyl oligonucleotide.

In a further embodiment, the RISC inactivator of the invention comprisesan oligonucleotide containing at least one locked nucleic acid (LNA).

In an additional embodiment, the RISC inactivator of the inventioncomprises an oligonucleotide containing at least one phosphorothioatemodification.

In another embodiment, the RISC inactivator (RISC inhibitor) of theinvention is modified with a moiety selected from the group consistingof the 2′-OH group replaced by a H, alkoxy or OR, halogen, SH, SR, amino(such as NH2, NHR, NR2,), or CN group, wherein R is lower alkyl,alkenyl, alkynyl, or aryl.

In one embodiment of the invention, the composition is a cell extract.

In a related embodiment, the composition is a Drosophila melanogastercell extract; and in another embodiment, the composition is specified tobe a Drosophila melanogaster embryo cell extract.

In an additional embodiment, the composition of the invention is aCaenorhabditis elegans cell extract.

In another embodiment, the composition of the invention is a mammaliancell extract.

The invention also enables detection of factors that associate with theRISC inactivator of the invention. In one embodiment, a RISC inactivatorsufficiently complementary to the guide strand of an siRNA or miRNA isattached to a surface and then contacted with a composition comprisingthe siRNA or miRNA, causing the RISC inactivator and siRNA or miRNA toform a complex also associated with other factors, such that factorsassociated with the RISC inactivator of the invention are detected.

In an additional embodiment, the RISC inactivator of the invention isnuclease-resistant.

In a further embodiment, the RISC inactivator of the invention isribonuclease-resistant.

In a related embodiment, the RISC inactivator of the invention is a2′-O-methyl oligonucleotide.

In a further embodiment, the RISC inactivator of the invention comprisesan oligonucleotide containing at least one locked nucleic acid (LNA).

In an additional embodiment, the RISC inactivator of the inventioncomprises an oligonucleotide containing at least one phosphorothioatemodification.

In another embodiment, the RISC inactivator of the invention is modifiedwith a moiety selected from the group consisting of the 2′-OH groupreplaced by a H, alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR,NR2,), or CN group, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.

In an additional embodiment of the invention, the RISC inactivator ofthe invention is attached to the surface of a bead.

In another embodiment, the RISC inactivator of the invention is tetheredto the surface of a streptavidin-coated bead via a 5′ biotin linkage.

In another embodiment, the surface of the invention is a paramagneticbead surface.

In an additional embodiment, the surface of the invention is a column.

In another embodiment, the composition of the invention is a cellextract comprising an siRNA or miRNA.

The invention also provides a method for identifying the active miRNAsof a composition. Accordingly, in one embodiment, the invention involvesthe process of contacting, with a cell extract comprising miRNAs, aseries or array comprising RISC inactivators sufficiently complementaryto guide strands of potential miRNAs (wherein the series or array isrelatively enriched for oligonucleotides sufficiently complementary toguide strands of potential miRNAs, as compared to random or extantarrays or series of oligonucleotide, genomic, EST or mRNA sequences);and then detecting the association of cell extract miRNAs with the RISCinactivators, such that active miRNAs are identified.

In an additional embodiment, the RISC inactivator of the invention isnuclease-resistant.

In a further embodiment, the RISC inactivator of the invention isribonuclease-resistant.

In a related embodiment, the RISC inactivator of the invention is a2′-O-methyl oligonucleotide.

In a further embodiment, the RISC inactivator of the invention comprisesan oligonucleotide containing at least one locked nucleic acid (LNA).

In an additional embodiment, the RISC inactivator of the inventioncomprises an oligonucleotide containing at least one phosphorothioatemodification.

In another embodiment, the RISC inactivator of the invention is modifiedwith a moiety selected from the group consisting of the 2′-OH groupreplaced by a H, alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR,NR2,), or CN group, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.

In one embodiment, the cell extract is a Drosophila melanogaster cellextract; and in a related embodiment, the cell extract is specified tobe a Drosophila melanogaster embryo cell extract.

In an additional embodiment, the cell extract of the invention is aCaenorhabditis elegans cell extract.

In another embodiment, the cell extract of the invention is a mammaliancell extract.

In a further embodiment, the polynucleotides of the cell extract of theinvention are fluorescently labeled.

In a related embodiment, the polynucleotides of the cell extract of theinvention are radioactively labeled.

In an additional embodiment, the RNAs (e.g., uracil moieties ofpolyribonucleotides) of the cell extracts are fluorescently labeled.

In a related embodiment, the RNAs (e.g., uracil moieties ofpolyribonucleotides) of the cell extracts are radioactively labeled.

The invention also enables monitoring of the extent to whichsequence-specific inhibition of RNA silencing occurs. In one embodiment,the invention includes the procedure of contacting a cell expressing areporter RNA and containing an siRNA or miRNA sufficiently complementaryto the reporter RNA, with a RISC inactivator that is sufficientlycomplementary to the guide strand of the siRNA or miRNA, and thendetecting the cleavage state of the reporter RNA, with the cleavagestate of the reporter RNA thus indicating the level of sequence-specificinhibition of RNA silencing.

In a related embodiment, monitoring of the extent to whichsequence-specific inhibition of RNA silencing occurs is achieved bycontacting a cell extract containing a reporter RNA and an siRNA ormiRNA sufficiently complementary to the reporter RNA, with a RISCinactivator that is sufficiently complementary to the guide strand ofthe siRNA or miRNA, and then detecting the cleavage state of thereporter RNA.

In another embodiment, monitoring of the extent to whichsequence-specific inhibition of RNA silencing occurs is achieved bycontacting an organism expressing a reporter RNA and containing an siRNAor miRNA sufficiently complementary to the reporter RNA, with a RISCinactivator that is sufficiently complementary to the guide strand ofthe siRNA or miRNA, and then detecting the cleavage state of thereporter RNA.

In an additional embodiment, monitoring of the extent to whichsequence-specific inhibition of RNA silencing occurs is achieved bycontacting a cell expressing a reporter RNA and containing an siRNA ormiRNA sufficiently complementary to the reporter RNA, with a RISCinactivator that is sufficiently complementary to the guide strand ofthe siRNA or miRNA, and then detecting the level or activity of thepolypeptide encoded by the reporter RNA.

In a related embodiment, monitoring of the extent to whichsequence-specific inhibition of RNA silencing occurs is achieved bycontacting a cell extract containing a reporter RNA and an siRNA ormiRNA sufficiently complementary to the reporter RNA, with a RISCinactivator that is sufficiently complementary to the guide strand ofthe siRNA or miRNA, and then detecting the level or activity of thepolypeptide encoded by the reporter RNA.

In a further embodiment, monitoring of the extent to whichsequence-specific inhibition of RNA silencing occurs is achieved bycontacting an organism expressing a reporter RNA and containing an siRNAor miRNA sufficiently complementary to the reporter RNA, with a RISCinactivator that is sufficiently complementary to the guide strand ofthe siRNA or miRNA, and then detecting the level or activity of thepolypeptide encoded by the reporter RNA.

In an additional embodiment, the RISC inactivator of the invention isnuclease-resistant.

In a further embodiment, the RISC inactivator of the invention isribonuclease-resistant.

In a related embodiment, the RISC inactivator of the invention is a2′-O-methyl oligonucleotide.

In a further embodiment, the RISC inactivator of the invention comprisesan oligonucleotide containing at least one locked nucleic acid (LNA).

In an additional embodiment, the RISC inactivator of the inventioncomprises an oligonucleotide containing at least one phosphorothioatemodification.

In another embodiment, the RISC inactivator of the invention is modifiedwith a moiety selected from the group consisting of the 2′-OH groupreplaced by a H, alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR,NR2,), or CN group, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.

In an additional embodiment, the cell, cell extract or organism of theinvention is a Drosophila melanogaster cell, cell extract or organism.

In another embodiment, the cell, cell extract or organism of theinvention is a Caenorhabditis elegans cell, cell extract or organism.

In a further embodiment, the cell, cell extract or organism of theinvention is a mammalian cell, cell extract or organism.

In an additional embodiment, the reporter RNA of the invention isradioactively labeled.

In another embodiment, the reporter RNA of the invention isfluorescently labeled.

The invention also allows for the identification of compounds capable ofmodulating the interaction of a RISC inactivator with a miRNA or siRNA.Accordingly, in one embodiment of the invention, a compositioncontaining: a reporter RNA, a miRNA or siRNA sufficiently complementaryto the reporter RNA, and a RISC inactivator sufficiently complementaryto the guide strand of the miRNA or siRNA, are contacted with acompound. The cleavage state of the reporter RNA or the expression levelor activity of the polypeptide encoded by the reporter RNA thendetected, allowing for a compound that modulates the interaction of theRISC inactivator with a miRNA or siRNA to be identified.

In a related embodiment of the invention, the procedure to identifycompounds capable of modulating the interaction of a RISC inactivatorwith a miRNA or siRNA is performed by contacting a cell or cell extractcontaining: a reporter RNA, a miRNA or siRNA sufficiently complementaryto the reporter RNA, and a RISC inactivator sufficiently complementaryto the guide strand of the miRNA or siRNA, with a compound. The cleavagestate of the reporter RNA or the expression level or activity of thepolypeptide encoded by the reporter RNA then detected, allowing for acompound that modulates the interaction of the RISC inactivator with amiRNA or siRNA to be identified.

In an additional embodiment of the invention, the procedure to identifycompounds capable of modulating the interaction of a RISC inactivatorwith a miRNA or siRNA is performed by contacting an organism containing:a reporter RNA, a miRNA or siRNA sufficiently complementary to thereporter RNA, and a RISC inactivator sufficiently complementary to theguide strand of the miRNA or siRNA, with a compound. The cleavage stateof the reporter RNA or the expression level or activity of thepolypeptide encoded by the reporter RNA then detected, allowing for acompound that modulates the interaction of the RISC inactivator with amiRNA or siRNA to be identified.

In one embodiment, the test compound of the invention is selected fromthe group consisting of a small molecule, a peptide, a polynucleotide,an antibody or biologically active portion thereof, a peptidomimetic,and a non-peptide oligomer.

In an additional embodiment, the RISC inactivator of the invention isnuclease-resistant.

In a further embodiment, the RISC inactivator of the invention isribonuclease-resistant.

In a related embodiment, the RISC inactivator of the invention is a2′-O-methyl oligonucleotide.

In a further embodiment, the RISC inactivator of the invention comprisesan oligonucleotide containing at least one locked nucleic acid (LNA).

In an additional embodiment, the RISC inactivator of the inventioncomprises an oligonucleotide containing at least one phosphorothioatemodification.

In another embodiment, the RISC inactivator of the invention is modifiedwith a moiety selected from the group consisting of the 2′-OH groupreplaced by a H, alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR,NR2,), or CN group, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.

In an additional embodiment, the cell, cell extract or organism of theinvention is a Drosophila melanogaster cell, cell extract or organism.

In another embodiment, the cell, cell extract or organism of theinvention is a Caenorhabditis elegans cell, cell extract or organism.

In a further embodiment, the cell, cell extract or organism of theinvention is a mammalian cell, cell extract or organism.

In an additional embodiment, the reporter RNA of the invention isradioactively labeled.

In another embodiment, the reporter RNA of the invention isfluorescently labeled.

The invention also enables identification of compounds that modulate theinteraction of a factor associated with a (miRNA-RISC inactivator)complex. Accordingly, in one embodiment of the invention, a compositioncomprising a miRNA and a RISC inactivator sufficiently complementary tothe guide strand of the miRNA are contacted by a compound, and the RISCinactivator or miRNA and any associated factors are then enriched for,allowing identification of a compound that modulates the interaction ofa factor associated with the (miRNA-RISC inactivator) complex.

In a related embodiment of the invention, identification of a compoundthat modulates the interaction of a factor associated with a (siRNA-RISCinactivator) complex is performed. A composition comprising a siRNA anda RISC inactivator sufficiently complementary to the guide strand of thesiRNA are contacted by a compound, and the RISC inactivator or siRNA andany associated factors are then enriched for, allowing foridentification of a compound that modulates the interaction of a factorassociated with the (siRNA-RISC inactivator) complex.

In one embodiment, the test compound of the invention is selected fromthe group consisting of a small molecule, a peptide, a polynucleotide,an antibody or biologically active portion thereof, a peptidomimetic,and a non-peptide oligomer.

In an additional embodiment, the RISC inactivator of the invention isnuclease-resistant.

In a further embodiment, the RISC inactivator of the invention isribonuclease-resistant.

In a related embodiment, the RISC inactivator of the invention is a2′-O-methyl oligonucleotide.

In a further embodiment, the RISC inactivator of the invention comprisesan oligonucleotide containing at least one locked nucleic acid (LNA).

In an additional embodiment, the RISC inactivator of the inventioncomprises an oligonucleotide containing at least one phosphorothioatemodification.

In another embodiment, the RISC inactivator of the invention is modifiedwith a moiety selected from the group consisting of the 2′-OH groupreplaced by a H, alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR,NR2,), or CN group, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.

In a further embodiment, the levels or identities of factors associatedwith the (miRNA-RISC inactivator) or (siRNA-RISC inactivator) complexare compared to an appropriate control.

In another embodiment, the levels or identities of factors associatedwith the (miRNA-RISC inactivator) or (siRNA-RISC inactivator) complexare compared to levels or identities of factors associated with the(miRNA-RISC inactivator) or (siRNA-RISC inactivator) complex in theabsence of compound.

The invention additionally allows for measurement of the level of aprogrammed RISC for a gene. Accordingly, in one embodiment, a RISCinactivator sufficiently complementary to the guide strand of a siRNA ormiRNA is attached to a surface and contacted with a compositioncomprising a labeled siRNA or miRNA, such that the level of programmedRISC for a gene is detected.

In a further embodiment, the siRNA or miRNA of the invention isradioactively labeled.

In an additional embodiment, the siRNA or miRNA of the invention isfluorescently labeled.

In an additional embodiment, the RISC inactivator of the invention isnuclease-resistant.

In a further embodiment, the RISC inactivator of the invention isribonuclease-resistant.

In a related embodiment, the RISC inactivator of the invention is a2′-O-methyl oligonucleotide.

In a further embodiment, the RISC inactivator of the invention comprisesan oligonucleotide containing at least one locked nucleic acid (LNA).

In an additional embodiment, the RISC inactivator of the inventioncomprises an oligonucleotide containing at least one phosphorothioatemodification.

In another embodiment, the RISC inactivator of the invention is modifiedwith a moiety selected from the group consisting of the 2′-OH groupreplaced by a H, alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR,NR2,), or CN group, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.

In another embodiment, the surface of the invention is a bead.

In a further embodiment, the RISC inactivator of the invention istethered to a streptavidin bead via a 5′ biotin linkage.

In one embodiment, the surface of the invention is a paramagnetic bead.

In another embodiment, the surface of the invention is a column.

In an additional embodiment, the composition of the invention is a cellextract comprising a siRNA or miRNA.

In a preferred embodiment, the invention is a composition comprising aRISC inactivator.

In a related embodiment, the RISC inactivator of the composition isnuclease-resistant.

In another embodiment, the RISC inactivator of the composition isribonuclease-resistant.

In an additional embodiment, the RISC inactivator of the composition isa 2′-O-methyl oligonucleotide.

In a further embodiment, the RISC inactivator of the invention comprisesan oligonucleotide containing at least one locked nucleic acid (LNA).

In an additional embodiment, the RISC inactivator of the inventioncomprises an oligonucleotide containing at least one phosphorothioatemodification.

In a related embodiment, modification of the RISC inactivator isselected from the group consisting of the 2′-OH group replaced by a H,alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR, NR2,), or CNgroup, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.

In another embodiment, the compositon comprising a RISC inactivator alsocomprises a pharmaceutically acceptable carrier.

The invention also enables development of pharmaceutical compositions.Accordingly, one embodiment of the invention consists of a apharmaceutical composition comprising a RISC inactivator sufficientlycomplementary to the guide strand of an siRNA or miRNA.

In one embodiment of the invention, the RISC inactivator is betweenabout 10-100 nucleotides (or modified nucleotides; e.g., ribonucleotidesor modified ribonucleotides).

In a further embodiment of the invention, the RISC inactivator isbetween about 10-40 nucleotides (or modified nucleotides; e.g.,ribonucleotides or modified ribonucleotides).

In an additional embodiment of the invention, the RISC inactivator isbetween about 15-35 nucleotides (or modified nucleotides; e.g.,ribonucleotides or modified ribonucleotides).

In another embodiment of the invention, the RISC inactivator is betweenabout 15-20 nucleotides (or modified nucleotides; e.g., ribonucleotidesor modified ribonucleotides).

In an alternative embodiment of the invention, the RISC inactivator isbetween about 20-25 nucleotides (or modified nucleotides; e.g.,ribonucleotides or modified ribonucleotides).

In a further embodiment of the invention, the RISC inactivator isbetween about 25-30 nucleotides (or modified nucleotides; e.g.,ribonucleotides or modified ribonucleotides).

In another embodiment, the RISC inactivator of the invention is betweenabout 30-35 (31, 32, 33, 34, 35) nucleotides (or modified nucleotides;e.g., ribonucleotides or modified ribonucleotides).

In a further embodiment, the RISC inactivator of the invention isbetween about 35-40 nucleotides (or modified nucleotides; e.g.,ribonucleotides or modified ribonucleotides).

In another embodiment, the RISC inactivator is administered at about lownanomolar (e.g., about 0.1-20 nM) doses.

Another embodiment of the invention includes a pharmaceuticalcomposition comprising a compound identified by the methods of theinvention related to compound identification.

In an additional embodiment, a method for treating an RNA interferencedisease or disorder comprising administering any of the pharmaceuticalcompositions identified by the invention is addressed.

In a related embodiment, administration of the pharmaceuticalcomposition of the invention treats cancer.

In another embodiment, administration of the pharmaceutical compositionof the invention treats spinal muscular atrophy (SMA).

In a further embodiment, administration of the pharmaceuticalcomposition of the invention treats diabetes.

An additional aspect of the invention features a method for inhibitingHMGA2 expression comprising contacting a cell with a let-7polynucleotide or fragment thereof, such that HMGA2 expression isinhibited. A related aspect of the invention features a method forenhancing HMGA2 expression comprising contacting a cell that containslet-7 or a fragment thereof with a let-7-RISC inactivator (a RISCinactivator sufficiently complementary to the guide strand of let-7),such that HMGA2 expression is enhanced.

Another aspect of the invention features a method for inhibiting Dicerexpression comprising contacting a cell with a let-7 polynucleotide orfragment thereof, such that Dicer expression is inhibited. A relatedaspect of the invention features a method for enhancing Dicer expressioncomprising contacting a cell that contains let-7 or a fragment thereofwith a let-7-RISC inactivator (a RISC inactivator sufficientlycomplementary to the guide strand of let-7), such that Dicer expressionis enhanced.

An additional aspect of the invention features a method for identifyinga compound that modulates the interaction of let-7-RISC with a Dicertranscript, comprising contacting a cell containing let-7-RISC with atest compound and determining the expression level and/or activity ofDicer, such that a compound that modulates the interaction of let-7-RISCwith Dicer transcript is identified.

Another aspect of the invention features a method for identifying RNAsmodulated by an RNA silencing agent comprising contacting a cell thatcontains an RNA silencing agent with a RISC inactivator; comparing theRNA expression levels of the RISC inactivator-contacted cell with theRNA expression levels of a cell that is not contacted with the RISCinactivator; and identifying RNAs whose expression level is modulated bytreatment with the RISC inactivator, such that RNAs modulated by the RNAsilencing agent are identified.

A further aspect of the invention features a method for identifyingpolypeptides whose expression is modulated by an RNA silencing agentcomprising contacting a cell that contains an RNA silencing agent with aRISC inactivator, then comparing the polypeptide expression levels ofthe RISC inactivator-contacted cell with the polypeptide expressionlevels of a cell that is not contacted with the RISC inactivator, andidentifying polypeptides whose expression level is modulated bytreatment with the RISC inactivator, such that polypeptides whoseexpression is modulated by the RNA silencing agent are identified.

So that the invention may be more readily understood, certain terms arefirst defined.

The term “nucleoside” refers to a molecule having a purine or pyrimidinebase covalently linked to a ribose or deoxyribose sugar. Exemplarynucleosides include adenosine, guanosine, cytidine, uridine andthymidine. The term “nucleotide” refers to a nucleoside having one ormore phosphate groups joined in ester linkages to the sugar moiety.Exemplary nucleotides include nucleoside monophosphates, diphosphatesand triphosphates. The terms “polynucleotide” and “nucleic acidmolecule” are used interchangeably herein and refer to a polymer ofnucleotides joined together by a phosphodiester linkage between 5′ and3′ carbon atoms.

The term “RNA” or “RNA molecule” or “ribonucleic acid molecule” refersto a polymer of ribonucleotides. The term “DNA” or “DNA molecule” ordeoxyribonucleic acid molecule” refers to a polymer ofdeoxyribonucleotides. DNA and RNA can be synthesized naturally (e.g., byDNA replication or transcription of DNA, respectively). RNA can bepost-transcriptionally modified. DNA and RNA can also be chemicallysynthesized. DNA and RNA can be single-stranded (i.e., ssRNA and ssDNA,respectively) or multi-stranded (e.g., double stranded, i.e., dsRNA anddsDNA, respectively). “mRNA” or “messenger RNA” is single-stranded RNAthat specifies the amino acid sequence of one or more polypeptidechains. This information is translated during protein synthesis whenribosomes bind to the mRNA.

The term “nucleotide analog” or “altered nucleotide” or “modifiednucleotide” refers to a non-standard nucleotide, including non-naturallyoccurring ribonucleotides or deoxyribonucleotides. Preferred nucleotideanalogs are modified at any position so as to alter certain chemicalproperties of the nucleotide yet retain the ability of the nucleotideanalog to perform its intended function. Examples of positions of thenucleotide which may be derivitized include the 5 position, e.g.,5-(2-amino)propyl uridine, 5-bromo uridine, 5-propyne uridine,5-propenyl uridine, etc.; the 6 position, e.g., 6-(2-amino)propyluridine; the 8-position for adenosine and/or guanosines, e.g., 8-bromoguanosine, 8-chloro guanosine, 8-fluoroguanosine, etc. Nucleotideanalogs also include deaza nucleotides, e.g., 7-deaza-adenosine; 0- andN-modified (e.g., alkylated, e.g., N6-methyl adenosine, or as otherwiseknown in the art) nucleotides; and other heterocyclically modifiednucleotide analogs such as those described in Herdewijn, AntisenseNucleic Acid Drug Dev., 2000 Aug. 10(4):297-310.

Nucleotide analogs may also comprise modifications to the sugar portionof the nucleotides. For example the 2′ OH-group may be replaced by agroup selected from H, OR, R, F, Cl, Br, I, SH, SR, NH₂, NHR, NR₂, COOR,or OR, wherein R is substituted or unsubstituted C₁-C₆ alkyl, alkenyl,alkynyl, aryl, etc. Other possible modifications include those describedin U.S. Pat. Nos. 5,858,988, and 6,291,438.

The phosphate group of the nucleotide may also be modified, e.g., bysubstituting one or more of the oxygens of the phosphate group withsulfur (e.g., phosphorothioates), or by making other substitutions whichallow the nucleotide to perform its intended function such as describedin, for example, Eckstein, Antisense Nucleic Acid Drug Dev. 2000 Apr.10(2):117-21, Rusckowski et al. Antisense Nucleic Acid Drug Dev. 2000Oct. 10(5):333-45, Stein, Antisense Nucleic Acid Drug Dev. 2001 Oct.11(5): 317-25, Vorobjev et al. Antisense Nucleic Acid Drug Dev. 2001Apr. 11(2):77-85, and U.S. Pat. No. 5,684,143. Certain of theabove-referenced modifications (e.g., phosphate group modifications)preferably decrease the rate of hydrolysis of, for example,polynucleotides comprising said analogs in vivo or in vitro.

The term “oligonucleotide” refers to a short polymer of nucleotidesand/or nucleotide analogs.

As used herein, the term “RISC inactivator” or “RISC inhibitor” refersto a nucleic acid-based agent which inactivates or inhibits RISCfunction in a sequence-specific manner. In particular, the agentinactivates or inhibits the siRNA or miRNA components of a RISC complexin a sequence-specific manner, i.e., the agent inactivates or inhibits aRISC complex containing a siRNA or miRNA having a sequence complementary(i.e., sufficiently complementary) to the sequence of the agent, butdoes not affect (i.e., appreciably affect) the function of RISCcomplexes containing guide RNAs (i.e., siRNA guide strands or miRNAs)unrelated in sequence. The RISC inactivators or RISC inhibitors of theinvention are preferably resistant or refractory to RISC-directedendonucleolytic cleavage or translational control (i.e., the agents donot themselves act as RISC substrates, as would target mRNAs).Preferably the agent is modified to resist degradation (i.e.,degradation by cellular nucleases, in particular, ribonucleases).Preferably, the RISC inactivators or RISC inhibitors of the inventionact (or are effective) at a concentration (e.g., have an IC50) in thenanomolar range, for example, less than 500 nM, preferably less than 400nM, more preferably less than 300, 250, 200, 150, 100, 75, 50, 25, 10,5, 2 or 1 nM.

Preferred RISC inactivators (or RISC inhibitors) are modifiedoligonucleotides having a length of about 20 to 40 nucleotides (ornucleotide analogs), e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40 nucleotides (or nucleotideanalogs). In preferred embodiments, RISC inactivators (or RISCinhibitors) are modified oligonucleotides having a length of about 25 to35 nucleotides (or nucleotide analogs). In other embodiments, RISCinactivators (or RISC inhibitors) are modified oligonucleotides having alength of about 5 to 60 nucleotides (or nucleotide analogs), or forexample, about 5-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-45,45-50, 50-55, 55-60, 60 or more nucleotides (or nucleotide analogs).

The term “agent” and “compound” are used interchangeably herein.

As used herein, the term “nuclease-resistant oligonucleotide” refers toany oligonucleotide that has been modified to inhibit degradation byenzymes such as, for example, the exonucleases known to be present inthe cytoplasm of a eukaryotic cell. RNA molecules (e.g., RNAoligonucleotides) are particularly at risk of degradation when combinedwith a composition comprising a cell extract or when introduced to acell or organism, and a “ribonuclease-resistant” oligonucleotide is thusdefined as a RISC inactivator that is relatively resistant toribonuclease enzymes (e.g., exonucleases), as compared to an unmodifiedform of the same oligonucleotide. Preferred RISC inactivators of theinvention include those that have been modified to render theoligonucleotide relatively nuclease-resistant or ribonuclease-resistant.In a preferred embodiment, the RISC inactivator of the invention hasbeen modified with a 2′-O-methyl group.

The term “2′-O-methyl oligonucleotide”, as used herein, possesses itsart-recognized meaning.

The term “RNA interference” or “RNAi” (also referred to in the art as“gene silencing” and/or “target silencing”, e.g., “target mRNAsilencing”), as used herein, refers generally to a sequence-specific orselective process by which a target molecule (e.g., a target gene,protein or RNA) is downregulated. In specific embodiments, the processof “RNA interference” or “RNAi” features degradation orpost-transcriptional silencing of RNA molecules, e.g., RNA moleculeswithin a cell, said degradation or silencing being triggered by an RNAiagent. Degradation and post-transcriptional silencing of target RNA iscatalyzed by an enzymatic, RNA-induced silencing complex (RISC). RNAioccurs in cells naturally to remove foreign RNAs (e.g., viral RNAs).Natural RNAi proceeds via fragments cleaved from free dsRNA which directthe degradative mechanism to other similar RNA sequences. Alternatively,RNAi can be initiated by the hand of man, for example, to silence theexpression of target genes.

The term “RNA silencing agent”, as used herein, refers to an RNA (oranalog thereof), having sufficient sequence complementarity to a targetRNA (i.e., the RNA being degraded) to direct RNA silencing (e.g., RNAi).An RNA silencing agent having a “sequence sufficiently complementary toa target RNA sequence to direct RNA silencing” means that the RNAsilencing agent has a sequence sufficient to trigger the destruction orpost-transcriptional silencing of the target RNA by the RNA silencingmachinery (e.g., the RISC) or process. An RNA silencing agent having a“sequence sufficiently complementary to a target RNA sequence to directRNA silencing” is also intended to mean that the RNA silencing agent hasa sequence sufficient to trigger the translational inhibition of thetarget RNA by the RNA silencing machinery or process. An RNA silencingagent having a “sequence sufficiently complementary to a target RNAencoded by the target DNA sequence such that the target DNA sequence ischromatically silenced” means that the RNA silencing agent has asequence sufficient to induce transcriptional gene silencing, e.g., todown-modulate gene expression at or near the target DNA sequence, e.g.,by inducing chromatin structural changes at or near the target DNAsequence.

As used herein, the term “small interfering RNA” (“siRNA”) (alsoreferred to in the art as “short interfering RNAs”) refers to an RNA (orRNA analog) comprising between about 10-50 nucleotides (or nucleotideanalogs) which is capable of directing or mediating RNA interference.

As used herein, the term “microRNA” (“miRNA”) refers to an RNA (or RNAanalog) comprising the product of an endogenous, non-coding gene whoseprecursor RNA transcripts can form small stem-loops from which maturemiRNAs are cleaved by Dicer (Lagos-Quintana et al., 2001; Lau et al.,2001; Lee and Ambros, 2001; Lagos-Quintana et al., 2002; Mourelatos etal., 2002; Reinhart et al., 2002; Ambros et al., 2003; Brennecke et al.,2003b; Lagos-Quintana et al., 2003; Lim et al., 2003a; Lim et al.,2003b). miRNAs are encoded in genes distinct from the mRNAs whoseexpression they control. Mature miRNAs represent the single strandedproduct of Dicer cleavage that then function as guide RNA fragments inmediating RNA silencing when incorporated into RISC.

As used herein, the term “antisense strand” of an siRNA or RNA silencingagent refers to a strand that is substantially complementary to asection of about 10-50 nucleotides, e.g., about 15-30, 16-25, 18-23 or19-22 nucleotides of the mRNA of the gene targeted for silencing. Theantisense strand or first strand has sequence sufficiently complementaryto the desired target mRNA sequence to direct target-specific RNAsilencing, (e.g., for RNAi, complementarity sufficient to trigger thedestruction of the desired target mRNA by the RNAi machinery orprocess). The term “sense strand” or “second strand” of an siRNA or RNAiagent refers to a strand that is complementary to the antisense strandor first strand. Antisense and ssense strands can also be referred to asfirst or second strands, the first or second strand havingcomplementarity to the target sequence and the respective second orfirst strand having complementarity to said first or second strand.

As used herein, the “5′ end”, as in the 5′ end of an antisense strand,refers to the 5′ terminal nucleotides, e.g., between one and about 5nucleotides at the 5′ terminus of the antisense strand. As used herein,the “3′ end”, as in the 3′ end of a sense strand, refers to the region,e.g., a region of between one and about 5 nucleotides, that iscomplementary to the nucleotides of the 5′ end of the complementaryantisense strand

As used herein, the term “guide strand” refers to a strand of an RNAsilencing agent, e.g., an antisense strand of an siRNA duplex, thatenters into RISC and directs cleavage or translational silencing of thetarget mRNA.

An siRNA or miRNA “that directs RNA silencing of a gene” is an siRNA ormiRNA that has a sequence sufficiently complementary to the target mRNAencoded by a gene to trigger the post-transcriptional silencing ordestruction of the target mRNA by the RNAi machinery or process.

An RISC inactivator having a “sequence sufficiently complementary to aRNA silencing agent, e.g., to a miRNA sequence or of a siRNA sequence”means that the RISC inactivator has a sequence sufficient to inhibit theactivity of the RNA silencing agent, e.g., the miRNA or siRNA. RISCinactivators are preferably sufficiently complementary to miRNAsequences or to siRNA sequences, in particular, the guide-strand orantisense strand sequences of an siRNA.

The term “phosphorylated” means that at least one phosphate group isattached to a chemical (e.g., organic) compound. Phosphate groups can beattached, for example, to proteins or to sugar moieties via thefollowing reaction: free hydroxyl group+ phosphate donor→phosphate esterlinkage. The term “5′ phosphorylated” is used to describe, for example,polynucleotides or oligonucleotides having a phosphate group attachedvia ester linkage to the C5 hydroxyl of the 5′ sugar (e.g., the 5′ribose or deoxyribose, or an analog of same). Mono-, di-, andtriphosphates are common. Also intended to be included within the scopeof the invention are phosphate group analogs which function in the sameor similar manner as the mono-, di-, or triphosphate groups found innature (see e.g., exemplified analogs.)

As used herein, the term “isolated RNA” (e.g., “isolated ssRNA”,“isolated siRNA” or “isolated ss-siRNA”) refers to RNA molecules whichare substantially free of other cellular material, or culture mediumwhen produced by recombinant techniques, or substantially free ofchemical precursors or other chemicals when chemically synthesized.

A “target gene” is a gene whose expression is to be selectivelyinhibited or “silenced.” This silencing is achieved by cleaving ortranslationally silencing the mRNA of the target gene (also referred toherein as the “target mRNA”) by an siRNA or miRNA, e.g., an siRNA ormiRNA that is created from an engineered RNA precursor by a cell's RNAsilencing system. One portion or segment of a duplex stem of the RNAprecursor is an anti-sense strand that is complementary, e.g.,sufficiently complementary to trigger the destruction of the desiredtarget mRNA by the RNAi machinery or process, to a section of about 18to about 40 or more nucleotides of the mRNA of the target gene.

As used herein, the term “RISC” refers to the proteins andsingle-stranded polynucleotides that interact to recognize target RNAmolecules. Demonstrated components of RISC include Dicer, R2D2 and theArgonaute family of proteins, as well as the guide strands of siRNAs andmiRNAs. In the case of a RISC loaded with a single-stranded guide RNAderived from a siRNA, the RISC cleaves the target RNA molecule.

As used herein, the term “RNA silencing” refers to all forms ofRISC-mediated small RNA-directed silencing and includes both RNAi(siRNA-mediated cleavage of target mRNA) and miRNA-mediatedtranslational repression.

As used herein the term “compound” includes any reagent which is testedusing the assays of the invention to determine whether it modulates RNAiactivity. More than one compound, e.g., a plurality of compounds, can betested at the same time for their ability to modulate RNAi activity in ascreening assay.

In one embodiment, test compounds comprise any selection of the groupconsisting of a small molecule, a peptide, a polynucleotide, an antibodyor biologically active portion thereof, a peptidomimetic, and anon-pepdide oligomer.

The term “in vitro” has its art recognized meaning, e.g., involvingpurified reagents or extracts, e.g., cell extracts. The term “in vivo”also has its art recognized meaning, e.g., involving living cells, e.g.,immortalized cells, primary cells, cell lines, and/or cells in anorganism.

A gene “involved” in a disorder includes a gene, the normal or aberrantexpression or function of which effects or causes a disease or disorderor at least one symptom of said disease or disorder

Various methodologies of the invention include a step that involvescomparing a value, level, feature, characteristic, property, etc. to a“suitable control”, referred to interchangeably herein as an“appropriate control”. A “suitable control” or “appropriate control” isany control or standard familiar to one of ordinary skill in the artuseful for comparison purposes. In one embodiment, a “suitable control”or “appropriate control” is a value, level, feature, characteristic,property, etc. determined prior to performing an RNAi methodology, asdescribed herein. For example, a transcription rate, mRNA level,translation rate, protein level, biological activity, cellularcharacteristic or property, genotype, phenotype, etc. can be determinedprior to introducing an RNAi-modulatory agent (e.g., an oligonucleotide,compound, etc., that alters sequence-specific RNAi activity) of theinvention into a cell or organism. In another embodiment, a “suitablecontrol” or “appropriate control” is a value, level, feature,characteristic, property, etc. determined in a cell or organism, e.g., acontrol or normal cell or organism, exhibiting, for example, normaltraits. In yet another embodiment, a “suitable control” or “appropriatecontrol” is a predefined value, level, feature, characteristic,property, etc.

Various aspects of the invention are described in further detail in thefollowing subsections.

I. RISC Inactivators and RNA Molecules, e.g., siRNAs and miRNAs

The present invention features RISC inactivators, e.g., RISC inhibitorssuitable for use in modulating RNA silencing both in vitro and in vivo.In vivo methodologies are useful for both general RNA silencingmodulatory purposes as well as in therapeutic application in which RNAsilencing modulation ( e.g., inhibition) is desirable.

RISC inactivators of the invention are of any size and/or chemicalcomposition sufficient to inhibit RNA silencing, in particular, microRNA(miRNA)-mediated translational repression and/or siRNA-mediated RNAi. Inexemplary embodiments, the RISC inactivators are oligonucleotides ofbetween about 10-100 nucleotides (or modified nucleotides), preferablybetween about 10-40 nucleotides (or modified nucleotides) (e.g.,ribonucleotides or modified ribonucleotides), for example, between about15-35, e.g., about 15-20, 20-25, 25-30, 30-35 (31, 32, 33, 34, 35), or35-40 nucleotides (or modified nucleotides) (e.g., ribonucleotides ormodified ribonucleotides). RISC inactivators are preferablysufficiently-complementary to miRNA sequences or to siRNA sequences, inparticular, the guide-strand or antisense strand sequences of an siRNA.

In exemplary embodiments of the invention, RISC inactivators compriseoligonucleotides that contain 2′-O-methyl modifications. Many otherforms of oligonucleotide modification may be used to generate RISCinactivators, including, for example, locked nucleic acids(oligonucleotides comprising at least one 2′-C,4′-C-oxy-methylene-linkedbicyclic ribonucleotide monomer) and phosphorothioate modifications,with one of skill in the art recognizing other modifications capable ofrendering an oligonucleotide an effective RISC inactivator.

The present invention also features RNAi agents, for example“single-stranded small interfering RNA molecules” (“ss-siRNA molecules”or “ss-siRNA”), methods of making said RNAi agents, e.g., ss-siRNAmolecules, and methods (e.g., research and/or therapeutic methods) forusing said RNAi agents, e.g., ss-siRNA molecules. Preferably, thess-siRNA molecule has a length from about 10-50 or more nucleotides.More preferably, the ss-siRNA molecule has a length from about 15-45nucleotides. Even more preferably, the ss-siRNA molecule has a lengthfrom about 19-40 nucleotides. The ss-siRNA molecules of the inventionfurther have a sequence that is “sufficiently complementary” to a targetmRNA sequence to direct target-specific RNA interference (RNAi), asdefined herein, i.e., the ss-siRNA has a sequence sufficient to triggerthe destruction of the target mRNA by the RNAi machinery or process. Thess-siRNA molecule can be designed such that every residue iscomplementary to a residue in the target molecule. Alternatively,substitutions can be made within the molecule to increase stabilityand/or enhance processing activity of said molecule. Substitutions canbe made within the strand or can be made to residues a the ends of thestrand. The 5′-terminus is, most preferably, phosphorylated (i.e.,comprises a phosphate, diphosphate, or triphosphate group). Contrary toprevious findings, however, that the 3′ end of an siRNA be a hydroxylgroup in order to facilitate RNAi, the present inventors havedemonstrated that there is no requirement for a 3′ hydroxyl group whenthe active agent is a ss-siRNA molecule. Accordingly, the inventionfeatures, in particular, ss-siRNA molecules wherein the 3′ end (i.e., C3of the 3′ sugar) lacks a hydroxyl group (i.e., ss-siRNA moleculeslacking a 3′ hydroxyl or C3 hydroxyl on the 3′ sugar (e.g., ribose ordeoxyribose).

The target RNA cleavage reaction guided by siRNAs (e.g., by ss-siRNAs)is highly sequence specific. In general, siRNA containing a nucleotidesequences identical to a portion of the target gene are preferred forinhibition. However, 100% sequence identity between the siRNA and thetarget gene is not required to practice the present invention. Thus theinvention has the advantage of being able to tolerate sequencevariations that might be expected due to genetic mutation, strainpolymorphism, or evolutionary divergence. For example, siRNA sequenceswith insertions, deletions, and single point mutations relative to thetarget sequence have also been found to be effective for inhibition.Alternatively, siRNA sequences with nucleotide analog substitutions orinsertions can be effective for inhibition. In addition, active miRNAsare characteristically not 100% complementary to their target mRNAs, anattribute proposed to explain their tendency to act throughtranslational repression, rather than cleavage, of their target mRNAs.

Sequence identity may be determined by sequence comparison and alignmentalgorithms known in the art. To determine the percent identity of twonucleic acid sequences (or of two amino acid sequences), the sequencesare aligned for optimal comparison purposes (e.g., gaps can beintroduced in the first sequence or second sequence for optimalalignment). The nucleotides (or amino acid residues) at correspondingnucleotide (or amino acid) positions are then compared. When a positionin the first sequence is occupied by the same residue as thecorresponding position in the second sequence, then the molecules areidentical at that position. The percent identity between the twosequences is a function of the number of identical positions shared bythe sequences (i.e., % homology=# of identical positions/total# ofpositions×100), optionally penalizing the score for the number of gapsintroduced and/or length of gaps introduced.

The comparison of sequences and determination of percent identitybetween two sequences can be accomplished using a mathematicalalgorithm. In one embodiment, the alignment generated over a certainportion of the sequence aligned having sufficient identity but not overportions having low degree of identity (i.e., a local alignment). Apreferred, non-limiting example of a local alignment algorithm utilizedfor the comparison of sequences is the algorithm of Karlin and Altschul(1990) Proc. Natl. Acad. Sci. USA 87:2264-68, modified as in Karlin andAltschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-77. Such an algorithmis incorporated into the BLAST programs (version 2.0) of Altschul, etal. (1990) J. Mol. Biol. 215:403-10.

In another embodiment, the alignment is optimized by introducingappropriate gaps and percent identity is determined over the length ofthe aligned sequences (i.e., a gapped alignment). To obtain gappedalignments for comparison purposes, Gapped BLAST can be utilized asdescribed in Altschul et al., (1997) Nucleic Acids Res.25(17):3389-3402. In another embodiment, the alignment is optimized byintroducing appropriate gaps and percent identity is determined over theentire length of the sequences aligned (i.e., a global alignment). Apreferred, non-limiting example of a mathematical algorithm utilized forthe global comparison of sequences is the algorithm of Myers and Miller,CABIOS (1989). Such an algorithm is incorporated into the ALIGN program(version 2.0) which is part of the GCG sequence alignment softwarepackage. When utilizing the ALIGN program for comparing amino acidsequences, a PAM120 weight residue table, a gap length penalty of 12,and a gap penalty of 4 can be used.

Greater than 70% sequence identity, e.g., 70%, 71%, 72%, 73%, 74%, 75%,76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or even 100% sequenceidentity, between the RNAi-inhibitory agent and the RNAi agent, e.g.,siRNA or miRNA, is preferred. Alternatively, the RNAi agent may bedefined functionally as a nucleotide sequence (or oligonucleotidesequence) a portion of which is capable of hybridizing with the RNAiagent (e.g., 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50° C. or 70°C. hybridization for 12-16 hours; followed by washing). Additionalpreferred hybridization conditions include hybridization at 70° C. in1×SSC or 50° C. in 1×SSC, 50% formamide followed by washing at 70° C. in0.3×SSC or hybridization at 70° C. in 4×SSC or 50° C. in 4×SSC, 50%formamide followed by washing at 67° C. in 1×SSC. The hybridizationtemperature for hybrids anticipated to be less than 50 base pairs inlength should be 5-10° C. less than the melting temperature (Tm) of thehybrid, where Tm is determined according to the following equations. Forhybrids less than 18 base pairs in length, Tm(° C.)=2(# of A+Tbases)+4(# of G+C bases). For hybrids between 18 and 49 base pairs inlength, Tm(° C.)=81.5+16.6(log10[Na+])+0.41(% G+C)−(600/N), where N isthe number of bases in the hybrid, and [Na+] is the concentration ofsodium ions in the hybridization buffer ([Na+] for 1×SSC=0.165 M).Additional examples of stringency conditions for polynucleotidehybridization are provided in Sambrook, J., E. F. Fritsch, and T.Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y., chapters 9 and 11 andCurrent Protocols in Molecular Biology, 1995, F. M. Ausubel et al.,eds., John Wiley & Sons, Inc., sections 2.10 and 6.3-6.4, incorporatedherein by reference. The length of the identical nucleotide sequencesmay be at least about 10, 12, 15, 17, 20, 22, 25, 27, 30, 32, 35, 37,40, 42, 45, 47 or 50 bases.

Modifications

In a preferred aspect, the RNA molecules, e.g., siRNAs and miRNAs, andRISC inactivators of the present invention are modified to improvestability in serum or in growth medium for cell cultures. In order toenhance the stability, the 3′-residues may be stabilized againstdegradation, e.g., they may be selected such that they consist of purinenucleotides, particularly adenosine or guanosine nucleotides.Alternatively, substitution of pyrimidine nucleotides by modifiedanalogues, e.g., substitution of uridine by 2′-deoxythymidine istolerated and does not affect the efficiency of RNA interference. Forexample, the absence of a 2′ hydroxyl may significantly enhance thenuclease resistance of the ss-siRNAs in tissue culture medium.

In an especially preferred embodiment of the present invention the RNAmolecules, e.g., siRNAs and miRNAs, and/or RISC inactivators may containat least one modified nucleotide analogue. The nucleotide analogues maybe located at positions where the target-specific activity, e.g., theRNAi mediating activity is not substantially effected, e.g., in a regionat the 5′-end and/or the 3′-end of the RNA molecule. Particularly, theends may be stabilized by incorporating modified nucleotide analogues.

Preferred nucleotide analogues include sugar- and/or backbone-modifiedribonucleotides (i.e., include modifications to the phosphate-sugarbackbone). For example, the phosphodiester linkages of natural RNA maybe modified to include at least one of a nitrogen or sulfur heteroatom.In preferred backbone-modified ribonucleotides the phosphoester groupconnecting to adjacent ribonucleotides is replaced by a modified group,e.g., of phosphothioate group. In preferred sugar-modifiedribonucleotides, the 2′ OH-group is replaced by a group selected from H,OR, R, halo, SH, SR, NH₂, NHR, NR₂ or ON, wherein R is C₁-C₆ alkyl,alkenyl or alkynyl and halo is F, Cl, Br or I.

Also preferred are nucleobase-modified ribonucleotides, i.e.,ribonucleotides, containing at least one non-naturally occurringnucleobase instead of a naturally occurring nucleobase. Bases may bemodified to block the activity of adenosine deaminase. Exemplarymodified nucleobases include, but are not limited to, uridine and/orcytidine modified at the 5-position, e.g., 5-(2-amino)propyl uridine,5-bromo uridine; adenosine and/or guanosines modified at the 8 position,e.g., 8-bromo guanosine; deaza nucleotides, e.g., 7-deaza-adenosine; O-and N-alkylated nucleotides, e.g., N6-methyl adenosine are suitable. Itshould be noted that the above modifications may be combined. RNAsilencing agents of the invention also may be modified with chemicalmoieties (e.g., cholesterol) that improve the in vivo pharmacologicalproperties of the RNA silencing agents.

RNA molecules and RISC inactivators may be produced enzymatically or bypartial/total organic synthesis, any modified nibonucleotide can beintroduced by in vitro enzymatic or organic synthesis. In oneembodiment, a RNA molecule, e.g., siRNA or miRNA, or RISC inactivator isprepared chemically. Methods of synthesizing RNA and DNA molecules areknown in the art, in particular, the chemical synthesis methods as described in Verma and Eckstein (1998) Annul Rev. Biochem. 67:99-134. Inanother embodiment, a RNA molecule is prepared enzymatically. Forexample, a ds-siRNA can be prepared by enzymatic processing of a long dsRNA having sufficient complementarity to the desired target mRNA.Processing of long ds RNA can be accomplished in vitro, for example,using appropriate cellular lysates and ds-siRNAs can be subsequentlypurified by gel electrophoresis or gel filtration. ds-siRNA can then bedenatured according to art-recognized methodologies. In an exemplaryembodiment, RNA can be purified from a mixture by extraction with asolvent or resin, precipitation, electrophoresis, chromatography, or acombination thereof. Alternatively, the RNA may be used with no or aminimum of purification to avoid losses due to sample processing.Alternatively, the RNA molecules, e.g., single-stranded RNAs, and RISCinactivators can also be prepared by enzymatic transcription fromsynthetic DNA templates or from DNA plasmids isolated from recombinantbacteria. Typically, phage RNA polymerases are used such as T7, T3 orSP6 RNA polymerase (Milligan and Uhlenbeck (1989) Methods Enzymol.180:51-62). The RNA may be dried for storage or dissolved in an aqueoussolution. The solution may contain buffers or salts to inhibitannealing, and/or promote stabilization of the single strands.

In one embodiment, the target mRNA of an RNA silencing agent, e.g.,siRNA or miRNA, of the invention specifies the amino acid sequence of acellular protein (e.g., a nuclear, cytoplasmic, transmembrane, ormembrane-associated protein). In another embodiment, the target mRNA ofthe invention specifies the amino acid sequence of an extracellularprotein (e.g., an extracellular matrix protein or secreted protein). Asused herein, the phrase “specifies the amino acid sequence” of a proteinmeans that the mRNA sequence is translated into the amino acid sequenceaccording to the rules of the genetic code. The following classes ofproteins are listed for illustrative purposes: developmental proteins(e.g., adhesion molecules, cyclin kinase inhibitors, Wnt family members,Pax family members, Winged helix family members, Hox family members,cytokines/lymphokines and their receptors, growth/differentiationfactors and their receptors, neurotransmitters and their receptors);oncogene-encoded proteins (e.g., ABLI, BCLI, BCL2, BCL6, CBFA2, CBL,CSFIR, ERBA, ERBB, EBRB2, ETSI, ETSI, ETV6, FGR, FOS, FYN, HCR, HRAS,JUN, KRAS, LCK, LYN, MDM2, MLL, MYB, MYC, MYCLI, MYCN, NRAS, PIM I, PML,RET, SRC, TALI, TCL3, and YES); tumor suppressor proteins (e.g., APC,BRCA1, BRCA2, MADH4, MCC, NFI, NF2, RB I, TP53, and WTI); and enzymes(e.g., ACC synthases and oxidases, ACP desaturases and hydroxylases,ADP-glucose pyrophorylases, ATPases, alcohol dehydrogenases, amylases,amyloglucosidases, catalases, cellulases, chalcone synthases,chitinases, cyclooxygenases, decarboxylases, dextriinases, DNA and RNApolymerases, galactosidases, glucanases, glucose oxidases, granule-boundstarch synthases, GTPases, helicases, hernicellulases, integrases,inulinases, invertases, isomerases, kinases, lactases, lipases,lipoxygenases, lysozymes, nopaline synthases, octopine synthases,pectinesterases, peroxidases, phosphatases, phospholipases,phosphorylases, phytases, plant growth regulator synthases,polygalacturonases, proteinases and peptidases, pullanases,recombinases, reverse transcriptases, RUBISCOs, topoisomerases, andxylanases).

In a preferred aspect of the invention, the target mRNA molecule of anRNA silencing agent, e.g., siRNA or miRNA, of the invention specifiesthe amino acid sequence of a protein associated with a pathologicalcondition. For example, the protein may be a pathogen-associated protein(e.g., a viral protein involved in immunosuppression of the host,replication of the pathogen, transmission of the pathogen, ormaintenance of the infection), or a host protein which facilitates entryof the pathogen into the host, drug metabolism by the pathogen or host,replication or integration of the pathogen's genome, establishment orspread of infection in the host, or assembly of the next generation ofpathogen. Alternatively, the protein may be a tumor-associated proteinor an autoimmune disease-associated protein.

In one embodiment, the target mRNA molecule of the RNA silencing agent,e.g., siRNA or miRNA, of the invention specifies the amino acid sequenceof an endogenous protein (i.e., a protein present in the genome of acell or organism). In another embodiment, the target mRNA molecule ofthe invention specified the amino acid sequence of a heterologousprotein expressed in a recombinant cell or a genetically alteredorganism. In another embodiment, the target mRNA molecule of theinvention specified the amino acid sequence of a protein encoded by atransgene (i.e., a gene construct inserted at an ectopic site in thegenome of the cell). In yet another embodiment, the target mRNA moleculeof the invention specifies the amino acid sequence of a protein encodedby a pathogen genome which is capable of infecting a cell or an organismfrom which the cell is derived.

By inhibiting an RNA silencing agent which controls expression of suchproteins, valuable information regarding the function of said RNAsilencing agent and/or proteins and therapeutic benefits which may beobtained from said inhibition may be obtained.

In certain embodiments, inhibition of RNA silencing agents with RISCinactivators can be used to identify and/or monitor gene products thatare regulated by and/or associate with the RNA silencing agent. Inexemplary embodiments, RNA and/or protein expression levels of cells,tissues or organisms contacted with a RISC inactivator are compared withexpression levels of cells, tissues or organisms that have not beencontacted with the RISC inactivator. Such a comparison therebyidentifies the direct impact of inhibiting the RNA silencing agent onthose gene products whose expression levels are surveyed. Suchcomparisons can be used to discover additional components of the testedRNA silencing agent's signaling pathway. Comparisons of RISCinactivator-treated and untreated states can additionally includecomparison of such states in cells, tissues or organisms that expressand/or contain the RNA silencing agent with RNA silencing agent-treatedand untreated states in cells, tissues or organisms that do not normallyexpress or contain the RNA silencing agent. Performance of suchcomparisons can enhance the specificity and efficacy of such approachesto identify RNA silencing agent pathway components.

Expression levels of surveyed genes may be assessed by any of a widevariety of well known methods for detecting expression of a transcribednucleic acid or protein. Non-limiting examples of such methods includenucleic acid hybridization methods e.g., Northern blots and/or use ofnucleic acid arrays; nucleic acid amplification methods; immunologicalmethods for detection of proteins; protein purification methods; andprotein function or activity assays.

RNA expression levels can be assessed by preparing mRNA/cDNA (i.e. atranscribed polynucleotide) from a cell, tissue or organism, and byhybridizing the mRNA/cDNA with a reference polynucleotide which is acomplement of the assayed nucleic acid, or a fragment thereof. cDNA can,optionally, be amplified using any of a variety of polymerase chainreaction or in vitro transcription methods prior to hybridization withthe complementary polynucleotide; preferably, it is not amplified.Expression of one or more transcripts can also be detected usingquantitative PCR to assess the level of expression of the transcript(s).

A mixture of transcribed polynucleotides obtained from the assayedcells, tissues or organisms also can be contacted with a substrate,having fixed thereto a polynucleotide complementary to or homologouswith at least a portion (e.g. at least 7, 10, 15, 20, 25, 30, 40, 50,100, 500, or more nucleotide residues) of an assayed RNA e.g., an arrayof complementary polynucleotides (probes). If polynucleotidescomplementary to or homologous with multiple assayed RNAs aredifferentially detectable on the substrate (e.g. detectable usingdifferent chromophores, fluorophores or other tags, or fixed todifferent selected positions), then the levels of expression of aplurality of RNAs can be assessed simultaneously using a singlesubstrate (e.g. a “gene chip” array of polynucleotides fixed at selectedpositions). When a method of assessing RNA expression is used whichinvolves hybridization of one nucleic acid with another, it is preferredthat the hybridization be performed under stringent hybridizationconditions.

Because such methods rely on detection of a difference in expressionlevels of one or more RNAs, it is preferable that the level ofexpression of the RNA is significantly greater than the minimumdetection limit of the method used to assess expression in at least oneof the assayed cell populations, tissues or organisms.

When a plurality of RNAs are assayed, the level of expression of eachRNA in a test sample can be compared with a baseline level of expressionof each of the plurality of RNAs in a non-treated sample of the sametype, either in a single reaction mixture (i.e. using reagents, such asdifferent fluorescent probes, for each RNA) or in individual reactionmixtures corresponding to one or more of the RNAs. In an exemplaryembodiment, a significantly increased level of expression of at leastone of the plurality of RNAs in a RISC inactivator-treated cellpopulation, tissue or organism that contains an RNA silencing agent,relative to the corresponding levels in an untreated cell population,tissue or organism that contains an RNA silencing agent, is anindication that the assayed RNA and/or gene encoding the assayed RNA isrepressed by the inactivated RNA silencing agent, either directly orindirectly. Similarly, a significantly decreased level of expression ofat least one of the plurality of assayed RNAs in an RNA silencingagent-treated cell population, tissue or organism (that does not containthe RNA silencing agent prior to treatment), relative to thecorresponding levels of the assayed RNAs in an untreated cellpopulation, tissue or organism (that does not contain the RNA silencingagent), is an indication that the assayed RNA silencing agent repressesthe assayed RNA and/or gene encoding the assayed RNA (either directly orindirectly). In exemplary embodiments, the expression modulationobserved for assayed RNAs in one cell type (e.g., a cell containing anRNA silencing agent either treated or not treated with a RISCinactivator) may also be compared with the expression modulationobserved for the assayed RNAs in another cell type (e.g., a cell thatdoes not normally contain an RNA silencing agent, which is eithertreated or not treated with the RNA silencing agent). Such an approachcan be used to identify RNA silencing agent-modulated RNAs/genes witheven greater statistical confidence than approaches assessing treatmentof a single type of cell with a single agent. Performance of parallelassays/expression profiles of cells (e.g., assays in duplicate,triplicate, etc.) can also enhance the statistical confidence ofexpression profile results. When a plurality of RNAs are assayed, 1, 2,3, 4, 5, 8, 10, 12, 15, 20, 30, or 50 or more individual RNAs may beidentified as modulated by the RNA silencing agent and/or RISCinactivator.

In one embodiment, RNA molecules, e.g., siRNAs or miRNAs, and/or RISCinactivators are synthesized either in vivo, in situ, or in vitro.Endogenous RNA polymerase of the cell may mediate transcription in vivoor in situ, or cloned RNA polymerase can be used for transcription invivo or in vitro. For transcription from a transgene in vivo or anexpression construct, a regulatory region (e.g., promoter, enhancer,silencer, splice donor and acceptor, polyadenylation) may be used totranscribe the ss-siRNA, miRNA or RISC inactivator. Inhibition may betargeted by specific transcription in an organ, tissue, or cell type;stimulation of an environmental condition (e.g., infection, stress,temperature, chemical inducers); and/or engineering transcription at adevelopmental stage or age. A transgenic organism that expresses an RNAsilencing agent, e.g., ss-siRNA, from a recombinant construct may beproduced by introducing the construct into a zygote, an embryonic stemcell, or another multipotent cell derived from the appropriate organism.

II. Short Hairpin RNAs (shRNAs)

In certain featured embodiments, the invention provides shRNAs havingefficacy in mediating RNA silencing. In contrast to short siRNAduplexes, short hairpin RNAs (shRNAs) mimic the natural precursors ofmiRNAs and enter at the top of the RNA silencing pathway. For thisreason, shRNAs are believed to mediate RNA silencing more efficiently bybeing fed through the entire natural RNA silencing pathway.

Short Hairpin RNAs That Generate siRNAs

shRNAs have a single strand that forms a duplex stem including twoportions that are generally complementary, and a loop, that connects thetwo portions of the stem. In a preferred embodiment, short hairpin RNAsof the invention are artificial constructs engineered to deliver desiredsiRNAs.

In shRNAs of the invention, one portion of the duplex stem is a nucleicacid sequence that is complementary (or anti-sense) to the target mRNA.Thus, shRNAs include a duplex stem with two portions and a loopconnecting the two stem portions. The two stem portions are about 18 or19 to about 25, 30, 35, 37, 38, 39, or 40 or more nucleotides in length.When used in mammalian cells, the length of the stem portions should beless than about 30 nucleotides to avoid provoking non-specific responseslike the interferon pathway. In non-mammalian cells, the stem can belonger than 30 nucleotides. In fact, the stem can include much largersections complementary to the target mRNA (up to, and including theentire mRNA). The two portions of the duplex stem must be sufficientlycomplementary to hybridize to form the duplex stem. Thus, the twoportions can be, but need not be, fully or perfectly complementary. Inaddition, the two stem portions can be the same length, or one portioncan include an overhang of 1, 2, 3, or 4 nucleotides. The overhangingnucleotides can include, for example, uracils (Us), e.g., all Us. Theloop in the shRNAs can be 2, 3, 4, 5, 6, 7, 8, 9, or more, e.g., 15 or20, or more nucleotides in length.

shRNAs of the invention include the sequences of the desired siRNAduplex. The desired siRNA duplex, and thus both of the two stem portionsin the shRNA, are selected by methods known in the art.

A defining feature of the shRNAs of the invention is that as aconsequence of their length, sequence, and/or structure, they do notinduce sequence non-specific responses, such as induction of theinterferon response or apoptosis, or that they induce a lower level ofsuch sequence non-specific responses than long, double-stranded RNA(>150bp) that has been used to induce RNA silencing. For example, theinterferon response is triggered by dsRNA longer than 30 base pairs.

III. Transgenes Encoding RNA Silencing Agents

The RNA silencing agents (e.g., siRNAs, miRNAs, etc.) and RISCinactivators of the invention can be synthesized by standard methodsknown in the art, e.g., by use of an automated nucleic acid synthesizer(such as are commercially available from Biosearch, Applied Biosystems,etc.). The RNA silencing agents and RISC inactivators can be useddirectly as described herein. The RNA silencing agents can be deliveredto cells in vitro or in vivo in which it is desired to target a specificmRNA for destruction.

Moreover, certain RNA silencing agents (e.g., siRNAs) can be expressedfrom appropriate vectors by methods known in the field. A number ofmethods have been developed for delivering nucleic acid-based moleculesto cells. For example, for in vivo delivery, molecules can be injecteddirectly into a tissue site or administered systemically. In vitrodelivery includes methods known in the art such as electroporation andlipofection.

To achieve intracellular concentrations of the nucleic acid moleculesufficient to suppress expression of endogenous mRNAs, one can use, forexample, a recombinant DNA construct in which the oligonucleotide isplaced under the control of a strong Pol III (e.g., U6 or Pol III H1-RNApromoter) or Pol II promoter. The use of such a construct to transfecttarget cells in vitro or in vivo will result in the transcription ofsufficient amounts of the shRNA to lead to the production of an siRNAthat can target a corresponding mRNA sequence for cleavage by RNAi todecrease the expression of the gene encoding that mRNA. (Oralternatively, such a construct may be made to express a miRNA.) Forexample, a vector can be introduced in vivo such that it is taken up bya cell and directs the transcription of shRNA or miRNA. Such a vectorcan remain episomal or become chromosomally integrated, as long as itcan be transcribed to produce the desired shRNA or miRNA.

Such vectors can be constructed by recombinant DNA technology methodsknown in the art. Vectors can be plasmid, viral, or other vectors knownin the art such as those described herein, used for replication andexpression in mammalian cells or other targeted cell types. The nucleicacid sequences encoding the shRNAs or miRNAs of the invention can beprepared using known techniques. For example, two synthetic DNAoligonucleotides can be synthesized to create a novel gene encoding theentire shRNA or miRNA. The DNA oligonucleotides, which will pair,leaving appropriate ‘sticky ends’ for cloning, can be inserted into arestriction site in a plasmid that contains a promoter sequence (e.g., aPol III or a Pol III promoter) and appropriate terminator sequences 3′to the shRNA or miRNA sequences (e.g., a cleavage and polyadenylationsignal sequence from SV40 or a Pol III terminator sequence).

The invention also encompasses genetically engineered host cells thatcontain any of the foregoing expression vectors and thereby express thenucleic acid molecules of the invention in the host cell. The host cellscan be cultured using known techniques and methods (see, e.g., Cultureof Animal Cells (R.I. Freshney, Alan R. Liss, Inc. 1987); MolecularCloning, Sambrook et al. (Cold Spring Harbor Laboratory Press, 1989)).

Successful introduction of the vectors of the invention into host cellscan be monitored using various known methods. For example, transienttransfection can be signaled with a reporter, such as a fluorescentmarker, such as Green Fluorescent Protein (GFP). Stable transfection canbe indicated using markers that provide the transfected cell withresistance to specific environmental factors (e.g., antibiotics anddrugs), such as hygromycin B resistance, e.g., in insect cells and inmammalian cells.

IV. Methods of Introducing RNAs, RNA Silencing Agents, Vectors, and HostCells

Physical methods of introducing nucleic acids include injection of asolution containing the nucleic acid (e.g., RNA molecule and/or RNAsilencing agent), bombardment by particles covered by the nucleic acid(e.g., RNA molecule and/or RNA silencing agent), soaking the cell ororganism in a solution of the nucleic acid (e.g., RNA. molecule and/orRNA silencing agent), or electroporation of cell membranes in thepresence of the nucleic acid (e.g., RNA molecule and/or RNA silencingagent). A viral construct packaged into a viral particle wouldaccomplish both efficient introduction of an expression construct intothe cell and transcription of a RNA molecule or silencing agent encodedby an expression construct. Other methods known in the art forintroducing nucleic acids or nucleic acid-based agents to cells may beused, such as lipid-mediated carrier transport, chemical-mediatedtransport, such as calcium phosphate, and the like. Thus the nucleicacid-based agent may be introduced along with components that performone or more of the following activities: enhance uptake by the cell,inhibit annealing of single strands, stabilize the single strands, orother-wise increase inhibition of the target gene.

The nucleic acid-based agent may be directly introduced into the cell(i.e., intracellularly); or introduced extracellularly into a cavity,interstitial space, into the circulation of an organism, introducedorally, or may be introduced by bathing a cell or organism in a solutioncontaining the nucleic acid-based agent (e.g., RNA molecule and/or RNAsilencing agent). Vascular or extravascular circulation, the blood orlymph system, and the cerebrospinal fluid are sites where the nucleicacid-based agent (e.g., RNA molecule and/or RNA silencing agent) may beintroduced.

The cell with the target gene may be derived from or contained in anyorganism. The organism may a plant, animal, protozoan, bacterium, virus,or fungus. The plant may be a monocot, dicot or gymnosperm; the animalmay be a vertebrate or invertebrate. Preferred microbes are those usedin agriculture or by industry, and those that are pathogenic for plantsor animals. Fungi include organisms in both the mold and yeastmorphologies. Plants include Arabidopsis thaliana thaliana; field crops(e.g., alfalfa, barley, bean, corn, cotton, flax, pea, rape, nice, rye,safflower, sorghum, soybean, sunflower, tobacco, and wheat); vegetablecrops (e.g., asparagus, beet, broccoli, cabbage, carrot, cauliflower,celery, cucumber, eggplant, lettuce, onion, pepper, potato, pumpkin,radish, spinach, squash, taro, tomato, and zucchini); fruit and nutcrops (e.g., almond, apple, apricot, banana, black-berry, blueberry,cacao, cherry, coconut, cranberry, date, fajoa, filbert, grape, grapefruit, guava, kiwi, lemon, lime, mango, melon, nectarine, orange, papaya,passion fruit, peach, peanut, pear, pineapple, pistachio, plum,raspberry, strawberry, tangerine, walnut, and watermelon); andornamentals (e.g., alder, ash, aspen, azalea, birch, boxwood, camellia,carnation, chrysanthemum, elm, fir, ivy, jasmine, juniper, oak, palm,poplar, pine, redwood, rhododendron, rose, and rubber). Examples ofvertebrate animals include fish, mammal, cattle, goat, pig, sheep,rodent, hamster, mouse, rat, primate, and human; invertebrate animalsinclude nematodes, other worms, drosophila, and other insects.

The cell having the target gene may be from the germ line or somatic,totipotent or pluripotent, dividing or non-dividing, parenchyma orepithelium, immortalized or transformed, or the like. The cell may be astem cell or a differentiated cell. Cell types that are differentiatedinclude adipocytes, fibroblasts, myocytes, cardiomyocytes, endothelium,neurons, glia, blood cells, megakaryocytes, lymphocytes, macrophages,neutrophils, eosinophils, basophils, mast cells, leukocytes,granulocytes, keratinocytes, chondrocytes, osteoblasts, osteoclasts,hepatocytes, and cells of the endocrine or exocrine glands.

Depending on the particular target gene and the dose of RNA silencingagent delivered, this process may provide partial or complete loss offunction for the target gene. A reduction or loss of gene expression inat least 50%, 60%, 70%, 80%, 90%, 95% or 99% or more of targeted cellsis exemplary. Inhibition of gene expression refers to the absence (orobservable decrease) in the level of protein and/or mRNA product from atarget gene. Specificity refers to the ability to inhibit the targetgene without manifest effects on other genes of the cell. Theconsequences of inhibition can be confirmed by examination of theoutward properties of the cell or organism (as presented below in theexamples) or by biochemical techniques such as RNA solutionhybridization, nuclease protection, Northern hybridization, reversetranscription, gene expression monitoring with a microarray, antibodybinding, enzyme linked immunosorbent assay (ELISA), Western blotting,radioimmunoassay (RIA), other immunoassays, and fluorescence activatedcell analysis (FACS).

For RNA-mediated inhibition in a cell line or whole organism, geneexpression is conveniently assayed by use of a reporter or drugresistance gene whose protein product is easily assayed. Such reportergenes include acetohydroxyacid synthase (AHAS), alkaline phosphatase(AP), beta galactosidase (LacZ), beta glucoronidase (GUS),chloramphenicol acetyltransferase (CAT), green fluorescent protein(GFP), horseradish peroxidase (HRP), luciferase (Luc), nopaline synthase(NOS), octopine synthase (OCS), and derivatives thereof. Multipleselectable markers are available that confer resistance to ampicillin,bleomycin, chloramphenicol, gentarnycin, hygromycin, kanamycin,lincomycin, methotrexate, phosphinothricin, puromycin, and tetracyclin.Depending on the assay, quantitation of the amount of gene expressionallows one to determine a degree of inhibition which is greater than10%, 33%, 50%, 90%, 95% or 99% as compared to a cell not treatedaccording to the present invention. Lower doses of injected material andlonger times after administration of a RNAi agent may result ininhibition in a smaller fraction of cells (e.g., at least 10%, 20%, 50%,75%, 90%, or 95% of targeted cells). Quantitation of gene expression ina cell may show similar amounts of inhibition at the level ofaccumulation of target mRNA or translation of target protein. As anexample, the efficiency of inhibition may be determined by assessing theamount of gene product in the cell; mRNA may be detected with ahybridization probe having a nucleotide sequence outside the region usedfor the inhibitory double-stranded RNA, or translated polypeptide may bedetected with an antibody raised against the polypeptide sequence ofthat region.

The RNA silencing agent may be introduced in an amount which allowsdelivery of at least one copy per cell. Higher doses (e.g., at least 5,10, 100, 500 or 1000 copies per cell) of material may yield moreeffective inhibition; lower doses may also be useful for specificapplications.

The efficacy of RISC-inactivating agents of the invention can readily beassayed by detecting a decrease in or reversal of inhibition of geneexpression, as described herein.

V. Arrays:

Expression arrays can be generated by attaching single-stranded nucleicacid molecules, e.g., polynucleotide probes, to a substrate in atwo-dimensional matrix or array. Each single-stranded polynucleotideprobe can comprise at least 5, 10, 15, 20, 25, 30, 35, 40, or 50 or morecontiguous nucleotides. Arrays may contain probes for any number ofRNAs, from a single RNA to a comprehensive collection of probes for theentire transcriptome (including, e.g., variant splice forms and variantsequences) of the cell, tissue or organism that is assayed.

A. Preparation of Arrays

Arrays are known in the art and consist of a surface to which probesthat correspond in sequence to gene products (e.g., cDNAs, mRNAs, cRNAs,polypeptides, and fragments thereof), can be specifically hybridized orbound at a known position. The array can be a matrix in which eachposition represents a discrete binding site for a product encoded by agene (e.g., a protein or RNA), and in which binding sites are presentfor products of most or almost all of the genes in the organism'sgenome. In one embodiment, the “binding site” (hereinafter, “site”) is anucleic acid or nucleic acid analogue to which a particular cognate cDNAcan specifically hybridize. The nucleic acid or analogue of the bindingsite can be, e.g., a synthetic oligomer, a full-length cDNA, a less-thanfull length cDNA, or a gene fragment.

B. Preparing Nucleic Acid Molecules for Arrays

As noted above, the “binding site” to which a particular cognate cDNAspecifically hybridizes is usually a nucleic acid or nucleic acidanalogue attached at that binding site. These DNAs can be obtained by,e.g., polymerase chain reaction (PCR) amplification of gene segmentsfrom genomic DNA, cDNA (e.g., by RT-PCR), or cloned sequences. PCRprimers are chosen, based on the known sequence of the genes or cDNA,that result in amplification of unique fragments (i.e., fragments thatdo not share more than 10 bases of contiguous identical sequence withany other fragment on the array). Computer programs are useful in thedesign of primers with the required specificity and optimalamplification properties. See, e.g., Oligo version 5.0 (NationalBiosciences™). In the case of binding sites corresponding to very longgenes, it will sometimes be desirable to amplify segments near the 3′end of the gene so that when oligo-dT primed cDNA probes are hybridizedto the array, less-than-full length probes will bind efficiently.Typically each gene fragment on the array will be between about 50 bpand about 2000 bp, more typically between about 100 bp and about 1000bp, and usually between about 300 bp and about 800 bp in length. PCRmethods are well known and are described, for example, in Innis et al.eds., 1990, PCR Protocols: A Guide to Methods and Applications, AcademicPress Inc. San Diego, Calif., which is incorporated by reference in itsentirety. It will be apparent that computer controlled robotic systemsare useful for isolating and amplifying nucleic acids.

An alternative means for generating the nucleic acid molecules for thearray is by synthesis of synthetic polynucleotides or oligonucleotides,e.g., using N-phosphonate or phosphoramidite chemistries (Froehler etal. (1986) Nucleic Acid Res 14:5399-5407; McBride et al. (1983)Tetrahedron Lett. 24:245-248). Synthetic sequences are between about 15and about 500 bases in length, more typically between about 20 and about50 bases. In some embodiments, synthetic nucleic acids includenon-natural bases, e.g., inosine. As noted above, nucleic acid moleculeanalogues may be used as binding sites for hybridization. An example ofa suitable nucleic acid analogue is peptide nucleic acid (see, e.g.,Egholm et al. (1993) Nature 365:566-568; see also U.S. Pat. No.5,539,083).

In an alternative embodiment, the binding (hybridization) sites are madefrom plasmid or phage clones of genes, cDNAs (e.g., expressed sequencetags), or inserts therefrom (Nguyen et al. (1995) Genomics 29:207-209).In yet another embodiment, the polynucleotide of the binding sites isRNA.

C. Attaching Nucleic Acid Molecules to the Solid Surface

The nucleic acid molecule or analogue are attached to a solid support,which may be made from glass, plastic (e.g., polypropylene, nylon),polyacrylamide, nitrocellulose, or other materials. An example of amethod for attaching the nucleic acid molecules to a surface is byprinting on glass plates, as is described generally by Schena et al.(1995) Science 270:467-470, the contents of which are expresslyincorporated herein by reference. This method is especially useful forpreparing arrays of cDNA. See also DeRisi et al. (1996) Nature Genetics14:457-460; Shalon et al. (1996) Genome Res. 6:639-645; and Schena etal. (1995) Proc. Natl. Acad. Sci. USA 93:10539-11286. Each of theaforementioned articles is incorporated by reference in its entirety.

A second example of a method for making arrays is by making high-densityoligonucleotide arrays. Techniques are known for producing arrayscontaining thousands of oligonucleotides complementary to definedsequences, at defined locations on a surface using photolithographictechniques for synthesis in situ (see, Fodor et al., (1991) Science251:767-773; Pease et al., (1994) Proc. Natl. Acad. Sci. USA91:5022-5026; Lockhart et al. (1996) Nature Biotech 14:1675; U.S. Pat.Nos. 5,578,832; 5,556,752; and 5,510,270, each of which is incorporatedby reference in its entirety for all purposes) or other methods forrapid synthesis and deposition of defined oligonucleotides (Blanchard etal. (1996) Biosensors & Bioelectronics 11: 687-90). When these methodsare used, oligonucleotides (e.g., 20-mers) of known sequence aresynthesized directly on a surface such as a derivatized glass slide. Inone embodiment, the array produced is redundant, with severaloligonucleotide molecules per RNA. Oligonucleotide probes can be chosento detect alternatively spliced mRNAs.

Other methods for making arrays, e.g., by masking (Maskos and Southern,1992, Nuc. Acids Res. 20:1679-1684), may also be used. In principal, anytype of array, for example, dot blots on a nylon hybridization membrane(see Sambrook et al., Molecular Cloning—A Laboratory Manual (2nd Ed.),Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989,which is hereby incorporated in its entirety), could be used, although,as will be recognized by those of skill in the art, very small arrayswill be preferred because hybridization volumes will be smaller.

Another method for making arrays is to directly deposit the probe on tothe array surface. In such an embodiment probes will bind non-covalentlyor covalently to the array depending on the surface of the array andcharacteristics of the probe. In preferred embodiments the array has anepoxy coating on top of a glass microscope slide and the probe ismodified at the amino terminal by an amine group. This combination ofarray surface and probe modification results in the covalent binding ofthe probe. Other methods of coating the array surface include usingacrylamide, sialinization and nitrocellulose. There are several methodsfor direct deposit of the probes on to the array surface. In oneembodiment, the probes are deposited using a pin dispense technique. Inthis technique, pins deposit probes onto the surface either usingcontact or non-contact printing. One preferred embodiment is non-contactprinting using quill tip pins. Another embodiment uses piezo electricdispensing to deposit the probes.

Control composition may be present on the array including compositionscomprising oligonucleotides or polynucleotides corresponding to genomicDNA, housekeeping genes, negative and positive control genes, and thelike. These latter types of compositions are not “unique”, i.e., theyare “common.” In other words, they are calibrating or control geneswhose function is not to tell whether a particular “key” gene ofinterest is expressed, but rather to provide other useful information,such as background or basal level of expression. The percentage ofsamples which are made of unique oligonucleotides or polynucleotide thatcorrespond to the same type of gene is generally at least about 30%, andusually at least about 60% and more usually at least about 80%.

D. Generating Labeled Probes

Methods for preparing total and poly (A)+RNA are well known and aredescribed generally in Sambrook et al., supra. In one embodiment, RNA isextracted from cells of the various types of interest in this inventionusing guanidinium thiocyanate lysis followed by CsCl centrifugation(Chirgwin et al. (1979) Biochemistry 18:5294-5299). Poly(A)+RNA isselected by selection with oligo-dT cellulose (see Sambrook et al.,supra).

Labeled cDNA is prepared from mRNA by oligo dT-primed or random-primedreverse transcription, both of which are well known in the art (seee.g., Klug and Berger, (1987) Methods Enzymol. 152:316-325). Reversetranscription may be carried out in the presence of a dNTP conjugated toa detectable label, e.g., a radioactive or fluorescently labeled dNTP.Alternatively, isolated mRNA can be converted to labeled antisense RNAsynthesized by in vitro transcription of double-stranded cDNA in thepresence of labeled dNTPs (Lockhart et al. (1996) Nature Biotech.14:1675, the contents of which are expressly incorporated herein byreference). In alternative embodiments, the cDNA or RNA probe can besynthesized in the absence of detectable label and may be labeledsubsequently, e.g., by incorporating biotinylated dNTPs or rNTP, or somesimilar means (e.g., photo-cross-linking a psoralen derivative of biotinto RNAs), followed by addition of labeled streptavidin (e.g.,phycoerythrin-conjugated streptavidin) or the equivalent.

When fluorescently-labeled probes are used, many suitable fluorophoresare known, including fluorescein, lissamine, phycoerythrin, rhodamine(Perkin Elmer Cetus™), Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, FluorX(Amersham™) and others (see, e.g., Kricka (1992) Nonisotopic DNA ProbeTechniques, Academic Press San Diego, Calif.). It will be appreciatedthat pairs of fluorophores are chosen that have distinct emissionspectra so that they can be easily distinguished.

A label other than a fluorescent label may also be used. For example, aradioactive label, or a pair of radioactive labels with distinctemission spectra, can be used (see Zhao et al. (1995) Gene 156:207;Pietu et al. (1996) Genome Res. 6:492).

In one embodiment, labeled cDNA is synthesized by incubating a mixturecontaining 0.5 mM dGTP, dATP and dCTP plus 0.1 mM dTTP plus fluorescentdeoxyribonucleotides (e.g., 0.1 mM Rhodamine 110 UTP (Perken ElmerCetus) or 0.1 mM Cy3 dUTP (Amersham™)) with reverse transcriptase (e.g.,SuperScript TM. II, LTI Inc.) at 42° C. for 60 min.

E. Generation of Targets

In one detection method, the array of immobilized nucleic acidmolecules, or probes, is contacted with a target sample containingtarget nucleic acid molecules, to which a radioactive or flourescentlabel is attached. Target nucleic acid molecules hybridize to the probeson the array and any non-hybridized nucleic acid molecules are removed.For fluorescently labeled targets, the array containing the hybridizedtarget nucleic acid molecules are exposed to light which excites theflourescent label. The resulting fluorescent intensity, or brightness,is detected. Alternatively, for radioactively labeled targets, theemissions of the radioactive label are detected.

In one embodiment, the target cDNA is generated from RNA derived fromselected cell, tissue or organism samples (target samples). The cDNA maybe labeled with a molecule which specifically binds with a secondmolecule which is labeled with one of the detection labels mentionedabove for the detection of hybridization. In one embodiment, the cDNA issynthesized using a biotinylated dNTP. The biotinylated target cDNA isthen hybridized to the array. There is then a second hybridization usingstreptavidin labeled with an appropriate fluorphore. The streptavidinwill bind specifically to the biotinylated cDNA resulting in thedetection of cDNA hybridization to the probe. In another embodiment, thecDNA is synthesized using specific primer sequences which add a capturesequence as the cDNA is being synthesized. The cDNA with the capturesequence is hybridized to the probes on the array. A secondhybridization is performed using a fluorescently labeled molecule whichbinds specifically to the capture sequence. resulting in the detectionof cDNA hybridization to the probe. Detection can be visual or withcomputer assistance.

F. Hybridization to Arrays

Nucleic acid hybridization and wash conditions are chosen so that theprobe “specifically binds” or “specifically hybridizes” to a specificarray site, i.e., the probe hybridizes, duplexes or binds to a sequencearray site with a complementary nucleic acid sequence but does nothybridize to a site with a non-complementary nucleic acid sequence. Asused herein, one polynucleotide sequence is considered complementary toanother when, if the shorter of the polynucleotides is less than orequal to 25 bases, there are no mismatches using standard base-pairingrules or, if the shorter of the polynucleotides is longer than 25 bases,there is no more than a 5% mismatch. Preferably, the polynucleotides areperfectly complementary (no mismatches). It can easily be demonstratedthat specific hybridization conditions result in specific hybridizationby carrying out a hybridization assay including negative controls (see,e.g., Shalon et al., supra, and Chee et al., supra).

Optimal hybridization conditions will depend on the length (e.g.,oligomer versus polynucleotide greater than 200 bases) and type (e.g.,RNA, DNA, PNA) of labeled probe and immobilized polynucleotide oroligonucleotide. General parameters for specific (i.e., stringent)hybridization conditions for nucleic acid molecules are described inSambrook et al., supra, and in Ausubel et al., 1987, Current Protocolsin Molecular Biology, Greene Publishing and Wiley-Interscience, NewYork, which is incorporated in its entirety for all purposes. Suchstringent conditions are known to those skilled in the art and can befound in sections 6.3.1-6.3.6 of Current Protocols in Molecular Biology,John Wiley & Sons, N.Y. (1989). A non-limiting example of stringenthybridization conditions are hybridization in 6× sodium chloride/sodiumcitrate (SSC) at about 45° C., followed by one or more washes in0.2×SSC, 0.1% SDS at 50-65° C. Useful hybridization conditions are alsoprovided in, e.g., Tijessen, 1993, Hybridization With Nucleic AcidProbes, Elsevier Science Publishers B. V. and Kricka, 1992, NonisotopicDNA Probe Techniques, Academic Press San Diego, Calif.

G. Signal Detection and Data Analysis

When fluorescently labeled probes are used, the fluorescence emissionsat each site of a transcript array can be, preferably, detected byscanning confocal laser microscopy. In one embodiment, a separate scan,using the appropriate excitation line, is carried out for each of thetwo fluorophores used. Alternatively, a laser can be used that allowssimultaneous specimen illumination at wavelengths specific to the twofluorophores and emissions from the two fluorophores can be analyzedsimultaneously (see Shalon et al., 1996, A DNA array system foranalyzing complex DNA samples using two-color fluorescent probehybridization, Genome Research 6:639-645, which is incorporated byreference in its entirety for all purposes). The arrays may be scannedwith a laser fluorescent scanner with a computer controlled X-Y stageand a microscope objective. Sequential excitation of the twofluorophores is achieved with a multi-line, mixed gas laser and theemitted light is split by wavelength and detected with twophotomultiplier tubes. Fluorescence laser scanning devices 35 aredescribed in Schena et al., 1996, Genome Res. 6:639-645 and in otherreferences cited herein. Alternatively, the fiber-optic bundle describedby Ferguson et al., 1996, Nature Biotech. 14:1681-1684, may be used tomonitor mRNA abundance levels at a large number of sites simultaneously.

Signals are recorded and, in one embodiment, analyzed by computer, e.g.,using a 12 bit analog to digital board. In one embodiment the scannedimage is despeckled using a graphics program (e.g., Hijaak GraphicsSuite) and then analyzed using an image gridding program that creates aspreadsheet of the average hybridization at each wavelength at eachsite. If necessary, an experimentally determined correction for “crosstalk” (or overlap) between the channels for the two fluors may be made.For any particular hybridization site on the transcript array, a ratioof the emission of the two fluorophores can be calculated. The ratio isindependent of the absolute expression level of the cognate gene, but isuseful for genes whose expression is significantly modulated by drugadministration, gene deletion, or any other tested event. According tothe method of the invention, the relative abundance of an mRNA in twocells or cell lines is scored as a perturbation (i.e., the abundance isdifferent in the two sources of mRNA tested), or as not perturbed (i.e.,the relative abundance is the same). As used herein, a differencebetween the two sources of RNA of at least a factor of about 25% (RNAfrom one source is 25% more abundant in one source than the othersource), more usually about 50%, even more often by a factor of about 2(twice as abundant), 3 (three times as abundant) or 5 (five times asabundant) is scored as a perturbation. Present detection methods allowreliable detection of differences of an order of about 2-fold and above,but more sensitive methods are expected to be developed.

In many cases, in addition to identifying a perturbation as positive ornegative, it is advantageous to determine the magnitude of theperturbation. This can be carried out, as noted above, by calculatingthe ratio of the emission of the two fluorophores used for differentiallabeling, or by analogous methods that will be readily apparent to thoseof skill in the art.

In another embodiment, a single fluorophore is used and all of thehybridizations from the samples are detected at a single wave length. Inthis method, the samples are all compared with each other to determineexpression levels. The expression levels for the membrane associatedmolecules are determined by comparing fluorescence intensity values fromall of the samples from the same wavelength. There are several differentmethods used for data analysis using a single fluorphore forhybridization. One method is using global normalization. Briefly, theintensity values from all of the sequences are averaged for each sample.All of the sample intensity averages are then averaged to determine theexperimental intensity average. A correction factor is calculated foreach sample by dividing the experimental intensity average by the sampleaverages. All of the sequence intensity values are multiplied by thecorrection factor. Following normalization, the treated sample valuesare divided by the untreated sample values to determine the foldexpression change.

Another method to analyze the intensity values uses a nonparametricanalysis. Nonparametric statistical analysis of microarray data isperformed by Spearman Rank Analysis. In the first method, each gene isranked in order of measured fluorescence/radiolabel intensity withineach sample and ranks are compared between test samples and groupedcontrol samples. The statistical significance of each comparison isrecorded. In the second method, each gene is ranked in order of measuredfluorescence/radiolabel intensity across samples and ranks are comparedbetween test samples and grouped control samples. The statisticalsignificance of each comparison is recorded. For each method, each geneis counted for the number of test samples that had statistically higherrank than the control samples for each treatment.

VI. Methods of Treatment:

The present invention provides for both prophylactic and therapeuticmethods of treating a subject at risk of (or susceptible to) a disorderor having a disorder associated with aberrant or unwanted geneexpression or activity. “Treatment”, or “treating” as used herein, isdefined as the application or administration of a therapeutic agent(e.g., small RNA-inhibitory agent, e.g., siRNA-inhibitory agent) to apatient, or application or administration of a therapeutic agent to anisolated tissue or cell line from a patient, who has a disease ordisorder, a symptom of disease or disorder or a predisposition toward adisease or disorder, with the purpose to cure, heal, alleviate, relieve,alter, remedy, ameliorate, improve or affect the disease or disorder,the symptoms of the disease or disorder, or the predisposition towarddisease.

With regards to both prophylactic and therapeutic methods of treatment,such treatments may be specifically tailored or modified, based onknowledge obtained from the field of pharmacogenomics.“Pharmacogenomics”, as used herein, refers to the application ofgenomics technologies such as gene sequencing, statistical genetics, andgene expression analysis to drugs in clinical development and on themarket. More specifically, the term refers the study of how a patient'sgenes determine his or her response to a drug (e.g., a patient's “drugresponse phenotype”, or “drug response genotype”). Thus, another aspectof the invention provides methods for tailoring an individual'sprophylactic or therapeutic treatment with either the target genemolecules of the present invention or target gene modulators accordingto that individual's drug response genotype. Pharmacogenomics allows aclinician or physician to target prophylactic or therapeutic treatmentsto patients who will most benefit from the treatment and to avoidtreatment of patients who will experience toxic drug-related sideeffects.

1. Prophylactic Methods

In one aspect, the invention provides a method for preventing in asubject, a disease or condition associated with an aberrant or unwantedtarget gene expression or activity, by administering to the subject atherapeutic agent (e.g., a RISC inactivator). Exemplary embodimentsfeature methods for specifically inactivating an RNAi agent (e.g., ansiRNA) by administering a RISC inactivator of the present invention. Useof a RISC inactivator allows, for example, for temporal regulation of,e.g., siRNA treatment in a subject where such treatment is detrimentalif performed for extended duration. RISC inactivators of the inventionmay also be used therapeutically to inhibit aberrant or unwanted miRNAactivity. Subjects at risk for a disease which is caused or contributedto by aberrant or unwanted target gene expression or activity can beidentified by, for example, any or a combination of diagnostic orprognostic assays as described herein. Administration of a prophylacticagent can occur prior to the manifestation of symptoms characteristic ofthe target gene aberrancy, such that a disease or disorder is preventedor, alternatively, delayed in its progression. Depending on the type oftarget gene aberrancy, for example, a target gene, target gene agonistor target gene antagonist agent can be used for treating the subject.The appropriate agent can be determined based on screening assaysdescribed herein.

2. Therapeutic Methods

Another aspect of the invention pertains to methods of modulating targetgene expression, protein expression or activity for therapeuticpurposes. Accordingly, in an exemplary embodiment, the modulatory methodof the invention involves contacting a cell capable of expressing targetgene with a therapeutic agent (e.g., RISC inactivator) that is specificfor the small RNA which targets a gene or protein (e.g., is specific forthe small RNA, e.g., siRNA or miRNA, that targets an mRNA encoded bysaid gene or specifying the amino acid sequence of said protein) suchthat expression or one or more of the activities of target protein ismodulated. These modulatory methods can be performed in vitro (e.g., byculturing the cell with the agent) or, alternatively, in vivo (e.g., byadministering the agent to a subject). As such, the present inventionprovides methods of treating an individual afflicted with a disease ordisorder characterized by aberrant or unwanted expression or activity ofa target gene polypeptide or nucleic acid molecule. Inhibition of targetgene activity is desirable in situations in which target gene isabnormally unregulated and/or in which decreased target gene activity islikely to have a beneficial effect.

3. Pharmacogenomics

The therapeutic agents (e.g., RISC inactivator) of the invention can beadministered to individuals to treat (prophylactically ortherapeutically) disorders associated with aberrant or unwanted targetgene activity. In conjunction with such treatment, pharmacogenomics(i.e., the study of the relationship between an individual's genotypeand that individual's response to a foreign compound or drug) may beconsidered. Differences in metabolism of therapeutics can lead to severetoxicity or therapeutic failure by altering the relation between doseand blood concentration of the pharmacologically active drug. Thus, aphysician or clinician may consider applying knowledge obtained inrelevant pharmacogenomics studies in determining whether to administer atherapeutic agent as well as tailoring the dosage and/or therapeuticregimen of treatment with a therapeutic agent.

Pharmacogenomics deals with clinically significant hereditary variationsin the response to drugs due to altered drug disposition and abnormalaction in affected persons. See, for example, Eichelbaum, M. et al.(1996) Clin. Exp. Pharmacol. Physiol. 23(10-11): 983-985 and Linder, M.W. et al. (1997) Clin. Chem. 43(2):254-266. In general, two types ofpharmacogenetic conditions can be differentiated. Genetic conditionstransmitted as a single factor altering the way drugs act on the body(altered drug action) or genetic conditions transmitted as singlefactors altering the way the body acts on drugs (altered drugmetabolism). These pharmacogenetic conditions can occur either as raregenetic defects or as naturally-occurring polymorphisms. For example,glucose-6-phosphate dehydrogenase deficiency (G6PD) is a commoninherited enzymopathy in which the main clinical complication ishaemolysis after ingestion of oxidant drugs (anti-malarials,sulfonamides, analgesics, nitrofurans) and consumption of fava beans.

One pharmacogenomics approach to identifying genes that predict drugresponse, known as “a genome-wide association”, relies primarily on ahigh-resolution map of the human genome consisting of already knowngene-related markers (e.g., a “bi-allelic” gene marker map whichconsists of 60,000-100,000 polymorphic or variable sites on the humangenome, each of which has two variants.) Such a high-resolution geneticmap can be compared to a map of the genome of each of a statisticallysignificant number of patients taking part in a Phase II/III drug trialto identify markers associated with a particular observed drug responseor side effect. Alternatively, such a high resolution map can begenerated from a combination of some ten-million known single nucleotidepolymorphisms (SNPs) in the human genome. As used herein, a “SNP” is acommon alteration that occurs in a single nucleotide base in a stretchof DNA. For example, a SNP may occur once per every 1000 bases of DNA. ASNP may be involved in a disease process, however, the vast majority maynot be disease-associated. Given a genetic map based on the occurrenceof such SNPs, individuals can be grouped into genetic categoriesdepending on a particular pattern of SNPs in their individual genome. Insuch a manner, treatment regimens can be tailored to groups ofgenetically similar individuals, taking into account traits that may becommon among such genetically similar individuals.

Alternatively, a method termed the “candidate gene approach”, can beutilized to identify genes that predict drug response. According to thismethod, if a gene that encodes a drugs target is known (e.g., a targetgene polypeptide of the present invention), all common variants of thatgene can be fairly easily identified in the population and it can bedetermined if having one version of the gene versus another isassociated with a particular drug response.

As an illustrative embodiment, the activity of drug metabolizing enzymesis a major determinant of both the intensity and duration of drugaction. The discovery of genetic polymorphisms of drug metabolizingenzymes (e.g., N-acetyltransferase 2 (NAT 2) and cytochrome P450 enzymesCYP2D6 and CYP2C19) has provided an explanation as to why some patientsdo not obtain the expected drug effects or show exaggerated drugresponse and serious toxicity after taking the standard and safe dose ofa drug. These polymorphisms are expressed in two phenotypes in thepopulation, the extensive metabolizer (EM) and poor metabolizer (PM).The prevalence of PM is different among different populations. Forexample, the gene coding for CYP2D6 is highly polymorphic and severalmutations have been identified in PM, which all lead to the absence offunctional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quitefrequently experience exaggerated drug response and side effects whenthey receive standard doses. If a metabolite is the active therapeuticmoiety, PM show no therapeutic response, as demonstrated for theanalgesic effect of codeine mediated by its CYP2D6-formed metabolitemorphine. The other extreme are the so called ultra-rapid metabolizerswho do not respond to standard doses. Recently, the molecular basis ofultra-rapid metabolism has been identified to be due to CYP2D6 geneamplification.

Alternatively, a method termed the “gene expression profiling”, can beutilized to identify genes that predict drug response. For example, thegene expression of an animal dosed with a therapeutic agent of thepresent invention can give an indication whether gene pathways relatedto toxicity have been turned on.

Information generated from more than one of the above pharmacogenomicsapproaches can be used to determine appropriate dosage and treatmentregimens for prophylactic or therapeutic treatment an individual. Thisknowledge, when applied to dosing or drug selection, can avoid adversereactions or therapeutic failure and thus enhance therapeutic orprophylactic efficiency when treating a subject with a therapeuticagent, as described herein.

Therapeutic agents can be tested in an appropriate animal model. Forexample, a small RNA-inhibitory agent, e.g., siRNA-inhibitory agent asdescribed herein can be used in an animal model to determine theefficacy, toxicity, or side effects of treatment with said agent.Alternatively, a therapeutic agent can be used in an animal model todetermine the mechanism of action of such an agent. For example, anagent can be used in an animal model to determine the efficacy,toxicity, or side effects of treatment with such an agent.Alternatively, an agent can be used in an animal model to determine themechanism of action of such an agent.

VI. Pharmaceutical Compositions

The invention pertains to uses of the above-described agents fortherapeutic treatments as described infra. Accordingly, the modulatorsof the present invention can be incorporated into pharmaceuticalcompositions suitable for administration. Such compositions typicallycomprise the nucleic acid molecule, protein, antibody, or modulatorycompound and a pharmaceutically acceptable carrier. As used herein thelanguage “pharmaceutically acceptable carrier” is intended to includeany and all solvents, dispersion media, coatings, antibacterial andantifungal agents, isotonic and absorption delaying agents, and thelike, compatible with pharmaceutical administration. The use of suchmedia and agents for pharmaceutically active substances is well known inthe art. Except insofar as any conventional media or agent isincompatible with the active compound, use thereof in the compositionsis contemplated. Supplementary active compounds can also be incorporatedinto the compositions.

A pharmaceutical composition of the invention is formulated to becompatible with its intended route of administration. Examples of routesof administration include parenteral, e.g., intravenous, intradermal,subcutaneous, intraperitoneal, intramuscular, oral (e.g., inhalation),transdermal (topical), and transmucosal administration. Solutions orsuspensions used for parenteral, intradermal, or subcutaneousapplication can include the following components: a sterile diluent suchas water for injection, saline solution, fixed oils, polyethyleneglycols, glycerine, propylene glycol or other synthetic solvents;antibacterial agents such as benzyl alcohol or methyl parabens;antioxidants such as ascorbic acid or sodium bisulfite; chelating agentssuch as ethylenediaminetetraacetic acid; buffers such as acetates,citrates or phosphates and agents for the adjustment of tonicity such assodium chloride or dextrose. pH can be adjusted with acids or bases,such as hydrochloric acid or sodium hydroxide. The parenteralpreparation can be enclosed in ampoules, disposable syringes or multipledose vials made of glass or plastic.

Pharmaceutical compositions suitable for injectable use include sterileaqueous solutions (where water soluble) or dispersions and sterilepowders for the extemporaneous preparation of sterile injectablesolutions or dispersion. For intravenous administration, suitablecarriers include physiological saline, bacteriostatic water, CremophorEL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In allcases, the composition must be sterile and should be fluid to the extentthat easy syringability exists. It must be stable under the conditionsof manufacture and storage and must be preserved against thecontaminating action of microorganisms such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (for example, glycerol, propylene glycol, andliquid polyetheylene glycol, and the like), and suitable mixturesthereof. The proper fluidity can be maintained, for example, by the useof a coating such as lecithin, by the maintenance of the requiredparticle size in the case of dispersion and by the use of surfactants.Prevention of the action of microorganisms can be achieved by variousantibacterial and antifungal agents, for example, parabens,chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In manycases, it will be preferable to include isotonic agents, for example,sugars, polyalcohols such as manitol, sorbitol, sodium chloride in thecomposition. Prolonged absorption of the injectable compositions can bebrought about by including in the composition an agent which delaysabsorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions can be prepared by incorporating the activecompound in the required amount in an appropriate solvent with one or acombination of ingredients enumerated above, as required, followed byfiltered sterilization. Generally, dispersions are prepared byincorporating the active compound into a sterile vehicle which containsa basic dispersion medium and the required other ingredients from thoseenumerated above. In the case of sterile powders for the preparation ofsterile injectable solutions, the preferred methods of preparation arevacuum drying and freeze-drying which yields a powder of the activeingredient plus any additional desired ingredient from a previouslysterile-filtered solution thereof.

Oral compositions generally include an inert diluent or an ediblecarrier. They can be enclosed in gelatin capsules or compressed intotablets. For the purpose of oral therapeutic administration, the activecompound can be incorporated with excipients and used in the form oftablets, troches, or capsules. Oral compositions can also be preparedusing a fluid carrier for use as a mouthwash, wherein the compound inthe fluid carrier is applied orally and swished and expectorated orswallowed. Pharmaceutically compatible binding agents, and/or adjuvantmaterials can be included as part of the composition. The tablets,pills, capsules, troches and the like can contain any of the followingingredients, or compounds of a similar nature: a binder such asmicrocrystalline cellulose, gum tragacanth or gelatin; an excipient suchas starch or lactose, a disintegrating agent such as alginic acid,Primogel, or corn starch; a lubricant such as magnesium stearate orSterotes; a glidant such as colloidal silicon dioxide; a sweeteningagent such as sucrose or saccharin; or a flavoring agent such aspeppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds are delivered in theform of an aerosol spray from pressured container or dispenser whichcontains a suitable propellant, e.g., a gas such as carbon dioxide, or anebulizer.

Systemic administration can also be by transmucosal or transdermalmeans. For transmucosal or transdermal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Such penetrants are generally known in the art, and include, forexample, for transmucosal administration, detergents, bile salts, andfusidic acid derivatives. Transmucosal administration can beaccomplished through the use of nasal sprays or suppositories. Fortransdermal administration, the active compounds are formulated intoointments, salves, gels, or creams as generally known in the art.

The compounds can also be prepared in the form of suppositories (e.g.,with conventional suppository bases such as cocoa butter and otherglycerides) or retention enemas for rectal delivery.

In one embodiment, the active compounds are prepared with carriers thatwill protect the compound against rapid elimination from the body, suchas a controlled release formulation, including implants andmicroencapsulated delivery systems. Biodegradable, biocompatiblepolymers can be used, such as ethylene vinyl acetate, polyanhydrides,polyglycolic acid, collagen, polyorthoesters, and polylactic acid.Methods for preparation of such formulations will be apparent to thoseskilled in the art. The materials can also be obtained commercially fromAlza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions(including liposomes targeted to infected cells with monoclonalantibodies to viral antigens) can also be used as pharmaceuticallyacceptable carriers. These can be prepared according to methods known tothose skilled in the art, for example, as described in U.S. Pat. No.4,522,811.

It is especially advantageous to formulate oral or parenteralcompositions in dosage unit form for ease of administration anduniformity of dosage. Dosage unit form as used herein refers tophysically discrete units suited as unitary dosages for the subject tobe treated; each unit containing a predetermined quantity of activecompound calculated to produce the desired therapeutic effect inassociation with the required pharmaceutical carrier. The specificationfor the dosage unit forms of the invention are dictated by and directlydependent on the unique characteristics of the active compound and theparticular therapeutic effect to be achieved, and the limitationsinherent in the art of compounding such an active compound for thetreatment of individuals.

Toxicity and therapeutic efficacy of such compounds can be determined bystandard pharmaceutical procedures in cell cultures or experimentalanimals, e.g., for determining the LD50 (the dose lethal to 50% of thepopulation) and the ED50 (the dose therapeutically effective in 50% ofthe population). The dose ratio between toxic and therapeutic effects isthe therapeutic index and it can be expressed as the ratio LD50/ED50.Compounds that exhibit large therapeutic indices are preferred. Althoughcompounds that exhibit toxic side effects may be used, care should betaken to design a delivery system that targets such compounds to thesite of affected tissue in order to minimize potential damage touninfected cells and, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can beused in formulating a range of dosage for use in humans. The dosage ofsuch compounds lies preferably within a range of circulatingconcentrations that include the ED50 with little or no toxicity. Thedosage may vary within this range depending upon the dosage formemployed and the route of administration utilized. For any compound usedin the method of the invention, the therapeutically effective dose canbe estimated initially from cell culture assays. A dose may beformulated in animal models to achieve a circulating plasmaconcentration range that includes the EC50 (i.e., the concentration ofthe test compound which achieves a half-maximal response) as determinedin cell culture. Such information can be used to more accuratelydetermine useful doses in humans. Levels in plasma may be measured, forexample, by high performance liquid chromatography.

The pharmaceutical compositions can be included in a container, pack, ordispenser together with instructions for administration.

VII. Screening Assays

A number of preferred methods of the invention relate to identifyingand/or characterizing potential pharmacological agents, e.g.,identifying new pharmacological agents from a collection of testsubstances and/or characterizing mechanisms of action and/or sideeffects of known pharmacological agents.

The invention provides methods (also referred to herein as “screeningassays”) for identifying modulators, i.e., candidate or test compoundsor agents (e.g., peptides, peptidomimetics, peptoids, small molecules orother drugs) which (a) have a modulatory (e.g., stimulatory orinhibitory) effect on the activity of a RISC inactivator of theinvention or, more specifically, (b) have a modulatory effect on theinteractions of a RISC inactivator sufficiently complementary to ansiRNA or miRNA with the siRNA or miRNA to which the siRNA or miRNA iscomplementary or (c) have a modulatory effect on the interactions of aRISC inactivator-siRNA or RISC inactivator-miRNA complex with associatedfactors (e.g., peptide, protein, hormone, co-factor, or nucleic acid,such as RISC components or RISC-associated factors), or (d) elicit amodulatory effect on RNA silencing by impacting the activity of a RISCinactivator of the invention. Such assays typically comprise a reactionbetween a RISC inactivator of the invention, an siRNA or miRNA to whichthe RISC inactivator is sufficiently complementary, and one or moreassay components. The other components may be either the test compounditself, or any combination comprising test compound, reporter RNA,cells, cell extracts or organisms.

The test compounds of the present invention may be obtained from anyavailable source, including systematic libraries of natural and/orsynthetic compounds. Test compounds may also be obtained by any of thenumerous approaches in combinatorial library methods known in the art,including: biological libraries; peptoid libraries (libraries ofmolecules having the functionalities of peptides, but with a novel,non-peptide backbone which are resistant to enzymatic degradation butwhich nevertheless remain bioactive; see, e.g., Zuckermann et al., 1994,J. Med. Chem. 37:2678-85); spatially addressable parallel solid phase orsolution phase libraries; synthetic library methods requiringdeconvolution; the ‘one-bead one-compound’ library method; and syntheticlibrary methods using affinity chromatography selection. The biologicallibrary and peptoid library approaches are limited to peptide libraries,while the other four approaches are applicable to peptide, non-peptideoligomer or small molecule libraries of compounds (Lam, 1997, AnticancerDrug Des. 12:145).

Examples of methods for the synthesis of molecular libraries can befound in the art, for example in: DeWitt et al. (1993) Proc. Natl. Acad.Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Natl. Acad. Sci. USA91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al.(1993) Science 261:1303; Carrell et al. (1994) Angew. Chem. Int. Ed.Engl. 33:2059; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061;and in Gallop et al. (1994) J. Med. Chem. 37:1233.

Libraries of compounds may be presented in solution (e.g., Houghten,1992, Biotechniques 13:412-421), or on beads (Lam, 1991, Nature354:82-84), chips (Fodor, 1993, Nature 364:555-556), bacteria and/orspores, (Ladner, U.S. Pat. No. 5,223,409), plasmids (Cull et al, 1992,Proc Natl Acad Sci USA 89:1865-1869) or on phage (Scott and Smith, 1990,Science 249:386-390; Devlin, 1990, Science 249:404-406; Cwirla et al,1990, Proc. Natl. Acad. Sci. 87:6378-6382; Felici, 1991, J. Mol. Biol.222:301-310; Ladner, supra.).

In one embodiment, the library is a natural product library, e.g., alibrary produced by a bacterial, fungal, or yeast culture. In anotherpreferred embodiment, the library is a synthetic compound library.

In one embodiment, the invention provides assays for screening forcellular factors which bind to RISC inactivator-miRNA- or RISCinactivator-siRNA-loaded RISC. Determining the ability of the cellularfactor to directly bind to a protein can be accomplished, for example,by coupling the factor with a radioisotope, fluor or enzymatic labelsuch that binding of the factor to the complex (e.g., RISC) can bedetermined by detecting the labeled marker factor in a complex. Forexample, factors (e.g., cellular polypeptides or polynucleotides) can belabeled with ¹²⁵I, ³⁵S, ¹⁴C, or ³H, either directly or indirectly, andthe radioisotope detected by direct counting of radioemission or byscintillation counting. Alternatively, assay components can beenzymatically labeled with, for example, horseradish peroxidase,alkaline phosphatase, or luciferase, and the enzymatic label detected bydetermination of conversion of an appropriate substrate to product. Orfluorescent labeling of test factors may be performed to allow forfluorescence-based detection of factor binding.

In another embodiment, the invention provides assays for screeningcandidate or test compounds which modulate the association RISCinactivators of the invention with miRNAs or siRNAs, and thereby elicitan effect on RNA silencing. Screens for compounds that modulate RISCinactivator-miRNA, RISC inactivator-siRNA and/or RNA silencing activitycan be performed in a number of ways. In one aspect of the invention,assessment of the effect of a potential RNA silencing modulatory agent,e.g., a test compound, on RISC inactivator-miRNA interaction, RISCinactivator-siRNA interaction or RNAi activity, may be examined bysubjecting the compositions, cells, and cell extracts of the inventionto the potential RISC inactivator-miRNA interaction, RISCinactivator-siRNA interaction or RNA silencing modulatory agent in atube or related type of vessel. Screening of a library of compounds forthe purpose of performing a high-throughput examination of the effect(s)of a large number of compounds on the RISC inactivator-miRNAinteraction, RISC inactivator-siRNA interaction or RNA silencingactivity of the invention's compositions, cells, organisms and lysatescan also be performed, for example, in microwells. RISCinactivator-miRNA- and RISC inactivator-siRNA-containing compositions,cells, organisms, and lysates of the invention can also be screenedagainst a matrix of test compounds to identify compounds capable ofmodulating the interaction of RISC inactivators of the invention withmiRNAs or siRNAs.

Monitoring of RNA silencing in such screening assays can involve anumber of assay readouts, e.g., the cleavage state of a target reporterRNA, expression or activity level of the polypeptide encoded by thetarget reporter RNA.

Detection of the interaction of the RISC inactivators of the inventionwith other polypeptides and nucleic acids can be performed, for example,through use of chemical crosslinking and immunoprecipitation methods,isolation of complexes through affinity column methodologies, or otherart-recognized methods.

The skilled artisan will appreciate that the enumerated organisms arealso useful for practicing other aspects of the invention, e.g., makingtransgenic organisms as described infra.

This invention is further illustrated by the following examples whichshould not be construed as limiting. The contents of all references,patents and published patent applications cited throughout thisapplication are incorporated herein by reference.

EXAMPLES

The following materials, methods, and examples are illustrative only andnot intended to be limiting.

Materials and Methods for Examples 1-5

General Methods

Drosophila embryo lysate preparation, in vitro RNAi reactions, andcap-labeling of target RNAs were as described (Haley et al., 2003).Target RNAs were used at ˜3 nM concentration. Cleavage products of RNAireactions were analyzed by electrophoresis on 5% or 8% denaturingacrylamide gels. Gels were dried, exposed to image plates, then scannedwith a FLA-5000 phosphorimager (Fuji). Images were analyzed using ImageReader FLA-5000 version 1.0 (Fuji) and Image Gauge version 3.45 (Fuji).Data analysis was performed using Excel (Microsoft) and IgorPro 5.0(Wavemetrics).

siRNA and 2′-O-methyl Oligonucleotides

Synthetic siRNA (Dharmacon) was deprotected according to themanufacturer, annealed (Elbashir et al., 2001c; Elbashir et al., 2001d),and used at 50 nM final concentration unless otherwise noted.2′-O-methyl oligonucleotides (IDT or Dharmacon) were: 5′-CAU CAC GUA CGCGGA AUA CUU CGA AAU GUC C-3′ (SEQ ID NO: 1) and 5′-Bio-CAU CAC GUA CGCGGA AUA CUU CGA AAU GUC C-3′ (complementary to the Pp-luc siRNA sensestrand; SEQ ID NO: 2) 5′-GGA CAU UUC GAA GUA UUC CGC GUA CGU GAU G-3′(SEQ ID NO: 3) and 5′-Bio-A CAU UUC GAA GUA UUC CGC GUA CGU GAU GUU-3′(complementary to the Pp-luc anti-sense strand; SEQ ID NO: 4);5′-Bio-UCU UCA CUA UAC AAC CUA CUA CCU CAA CCU U-3′ (complementary tolet-7; SEQ ID NO: 5); 5′ Biotin was attached via a six-carbon spacerarm.

Immobilized 2′-O-methyl Oligonucleotide Capture of RISC

pmol biotinylated 2′-O-methyl oligonucleotide was incubated for 1 houron ice in lysis buffer containing 2 mM DTT with 50 μl Dynabeads M280 (asa suspension as provided by the manufacturer; Dynal) to immobilize theoligonucleotide on the beads. To ensure that the tetheredoligonucleotide remained in excess when more than 50 nM siRNA was used,20 pmol biotinylated 2′-O-methyl oligonucleotide was immobilized. ForRISC capture assays, siRNA was pre-incubated in a standard 50 μl invitro RNAi reaction for 15 minutes at 25° C. Then, the immobilized2′-O-methyl oligonucleotide was added to the reaction and incubationcontinued for 1 hour at 25° C. After incubation, beads were collectedusing a magnetic stand (Dynal). The unbound supernatant was recoveredand an aliquot assayed for RISC activity as previously described(Elbashir et al., 2001c; Nykänen et al., 2001) to confirm that RISCdepletion was complete. The beads were then washed three times withice-cold lysis buffer containing 0.1% (w/v) NP 40 and 2 mM DTT followedby a wash without NP 40. To determine the amount of RISC formed, inputand bound radioactivity was determined by scintillation counting(Beckman). To isolate let-7-containing complexes from C. elegans adults,20 pmol of immobilized 2′-O-methyl oligonucleotide was incubated with 1mg total protein.

Sequential Transfection

HeLa S3 cells were transfected in a 24-well plate (200 mm² per well)using Lipofectamine 2000 (GIBCO) according to the manufacturer'sprotocol first with various concentrations of siRNA targeting Pp-lucmRNA. After 6 hours the cells were washed with PBS and the mediareplaced. On the next day, the cells were cotransfected with Renillareniformis (Accession Number AF025846) (0.1 μg/well) and Photinuspyralis (Accession Number X65324) luciferase-expressing plasmids (0.25μg/well) and 2′-O-methyl oligonucleotides using Lipofectamine 2000(GIBCO) according to the manufacturer protocol. Twenty-four hours later,the luciferase activity was measured with the Dual Luciferase assay kit(Promega) using a Mediators PhL luminometer.

Worm Injection

For in vivo inhibition of let-7 function, 1 mg/ml let-7-complementary2′-Omethyl oligonucleotide in water (100 μM) was injected into eitherwild-type (N2) or lin-41(ma104) L2 larvae. Injection of L2 larvae wasessentially as described (Conte and Mello, 2003). The 2′-O-methyloligonucleotide solution was injected into the body cavity of the larvausing the low flow and pressure setting to prevent animals from dying.Despite these precautions, ˜60% of the animals do not survive injection,irrespective of the oligonucleotide injected. let-7 phenotypes were alsoobserved at 10 μM oligonucleotide, but were less penetrant. Phenotypeswere scored after the injected animals survived to adulthood.

Expression Profiling of RISC Inactivator- and let-7-Treated andUntreated Cells

Experiments were performed in triplicate for each state (HeLa cellstreated with let-7-RISC inactivator, untreated HeLa cells, NT2 cellstreated with let-7, untreated NT2 cells). Total RNA extracted fromsamples was used to generate cRNA target, subsequently hybridized tohuman U133A oligonucleotide probe arrays (purchased from Affymetrix,Santa Clara, Calif.). cRNA preparation was performed using theAffymetrix GeneChip® one-cycle cDNA synthesis kit followed by labelingwith the Affymetrix GeneChip® IVT labeling kit. Hybridization and dataanalysis was performed by the MIT microarray facility using standardmethods (see, e.g., Ruan et al. Diabetes 51, 3176-3188; Bhattacharjee etal. Proc. Natl. Acad. Sci. USA 98, 13790-13795; Golub et al. Science286, 531-537). All experimental expression profiles were normalized tothe expression profile of cells treated separately with a non-specific2′-O-methyl oligonucleotide and GFP siRNA.

Other Methods

Synchronized transgenic animals carrying GFP::ALG-1, GFP::ALG-2 wereharvested at adulthood and homogenized in ice-cold buffer (25 mMHEPES-NaOH (pH 7.4), 150 mM NaCl, 1 mM EDTA, 1 mM DTT, 10% (v/v)glycerol, 0.5% (v/v) Triton X-100, 2% (v/v) SUPERaseIn (Ambion) and MiniComplete Protease Inhibitor cocktail (1 tablet/10 ml solution) (Roche))using a stainless steel Dounce homogenizer (Wheaton). The homogenizedextract was clarified by a centrifugation at 13,817×g for 10 minutes at4° C.

To recover the proteins associated with the let-7 miRNA, the beads wereboiled for 10 minutes in 20 μl SDS loading buffer (10 mM Tris-HCl(pH6.8), 2% (w/v) SDS, 100 mM DTT and 10% (v/v) glycerol). Proteins wereresolved by SDS-PAGE on an 8% gel, and transferred to Hybond-C membrane(Amersham Biosciences). To detect GFP-tagged ALG-1, ALG-2, and RDE4proteins, the membrane was incubated overnight at 4° C. with eithermonoclonal anti-GFP (Roche) or an affinity purified polyclonalanti-RDE-4 antibody (Tabara et al, 2003) diluted 1:1000 intoTBST-milk-solution (100 mM Tris-HCl (pH 7.5), 150 mM NaCl, 0.1% (v/v)Tween-20 and 5% (w/v) dried milk), incubated 1 hr at room temperaturewith either anti-mouse (GFP-tagged ALG-1/ALG-2) or anti-rabbit (RDE-4)HRP- conjugated secondary antibody(Jackson Laboratories) diluted 1:5,000in TBST, then visualized by enhanced chemulinescence (NEN).

Immunoprecipitation of GFP-tagged ALG-1/ALG-2 complexes was performed bypre-clearing worm extract with 50 μl protein-G agarose beads (Roche) per5 mg total protein for 1 hr at 4° C. The cleared extract was thenincubated with 10 μg of monoclonal antibody anti-AFP 3E6 (Qbiogene) for1 hr at 4° C. followed by 50 μl protein-G agarose. The agarose beadswere then washed three times with ice-cold homogenization buffer.

Depletion of let-7 miRNA was monitored by Northern blotting. RNA waseluted from the immobilized 2′-O-methyl oligonucleotide by digestionwith 1 mg/ml proteinase K in 200 mM Tris-HCl (pH 7.5), 25 mM EDTA, 300mM NaCl, 2% (w/v) SDS) at 50° C for 30 min, followed by extraction withPhenol-Chloroform, and recovered by precipitation with ethanol.Recovered RNA was resuspended in 10 μl formamide loading buffer (98%(v/v) deionized formamide, 10 mM EDTA, 0.025% (w/v) xylene cyanol, 0.025% (w/v) bromophenol blue), heated to 100° C. for 2 min. RNA was resolvedon a 15% denaturing acrylamide gel, transferred to Hybond-N membrane(Amersham Biosciences), and detected by Northern analysis using a5′32P-radiolabeled anti-sense let-7 RNA probe (UAU ACA ACC UAC UAC CUCAUU; SEQ ID NO: 6) as described (Hutvágner and Zamore, 2002). For invivo inhibition of let-7 function, 1 mg/ml let-7-complementary2′-O-methyl oligonucleotide in water (100 μM) and injected into L2larvae of either wild-type (N2) or lin-41(ma104) strains. let-7phenotypes were also observed at 10 μM oligonucleotide, but were lesspenetrant. Phenotypes were scored when the injected animals reachedadulthood.

Example 1 Inhibition of RNAi by 2′-O-methyl Oligonucleotides

Although RNAi has proved a straightforward and cost-effective method toassess the function of protein-coding mRNAs (Fire et al., 1998; Caplenet al., 2000; Caplen et al., 2001; Carthew, 2001; Elbashir et al.,2001b) and even some non-coding RNAs (Liang et al., 2003), no comparablemethod allows the sequence-specific inactivation of the siRNA or miRNAcomponents of the RISC. The invention features such inhibitors.Preferred inhibitors of RISC function are nucleic acid-based moleculesthat are recognized by the RISC by nucleotide complementarity, but arerefractory to RISC-directed endonucleolytic cleavage or translationalcontrol. Such molecules are designed such that they are capable oftitrating out RISC complexes containing a complementary siRNA or miRNA,but have little or no effect on the function of RISC complexescontaining guide RNAs unrelated in sequence. Such RISC inhibitors canfurther be designed such that they are resistant to degradation bycellular ribonucleases so that they persist long enough to bind RISC andblock its function. Finally, inhibitors of small RNA function aredesigned such that they are capable of acting at concentrations unlikelyto elicit non-specific responses to the inhibitor itself, i.e., in thelow nanomolar range, the same concentration at which siRNAs themselvesare effective.

At micromolar concentration, DNA anti-sense oligonucleotides may blockmiRNA function in Drosophila embryos (Boutla et al., 2003), but the poorstability of DNA oligonucleotides in vivo may limit their utility.Phosphorothioate substituted DNA oligonucleotides, which show good invivo stability, do not inhibit RISC function in vitro (data not shown).2′-O-methyl oligonucleotides are also highly resistant to cellularribonucleases. To test if 2′-O-methyl oligonucleotides can act as RISCinhibitors, it was examined whether a 2′-O-methyl oligonucleotide,tethered to streptavidin paramagnetic beads via a 5′ biotin linkage,could be used to deplete siRNA-programmed RISC from the reaction.Drosophila embryo lysate was programmed with a synthetic siRNA duplexdirected against a firefly luciferase (Pp-luc) mRNA target (FIG. 1A).Then, a tethered 31-nucleotide 2′-O-methyl oligonucleotide complementaryto the 21 nucleotide siRNA strand was added. Finally, the beads wereremoved from the solution using a magnet, and the supernatant tested forsiRNA-programmed RISC activity. Under these conditions, the 2′-O-methyloligonucleotide completely depleted the reaction of RISC programmed withthe anti-sense strand of the siRNA, but not of RISC programmed with thesense strand (FIG. 1B). Thus, depletion occurred only when the siRNAstrand contained within RISC was complementary to the tetheredoligonucleotide.

This method was extended to measure the amount of RISC formed in the invitro reaction at different concentrations of the siRNA duplex. An siRNAduplex in which the anti-sense strand was 5′-³²P-radiolabeled wasincubated in the reaction, then the tethered 2′-O-methyl oligonucleotideadded to deplete the reaction of anti-sense siRNA-programmed RISC. Thebeads were then washed and the fraction of ³²P-siRNA bound to the beadsdetermined. Depletion was verified by testing the supernatant for RISCactivity. Formally, the amount of ³²P-siRNA retained on the beads for agiven concentration of siRNA duplex places an upper limit on theconcentration of RISC formed. However, the presently reported resultsusing this assay were, within error, identical to the amount of RISCmeasured by two independent methods: the accumulation of single-strandedsiRNA from functionally asymmetric siRNA duplexes (Schwarz et al.,2003), and the magnitude of the burst of target cleavage measured bypre-steady state kinetics (data not shown). The simplest explanation forthese results was that this assay directly measured siRNA incorporatedinto RISC. FIG. 2A shows the results of this assay for six differentconcentrations of siRNA duplex (5, 15, 25, 50, 100, 200 nM siRNA).First, the data show that RISC assembly in vitro was inefficient; themajority of siRNA duplexes did not contribute to RISC production.Second, RISC assembly was saturable, suggesting that some component ofRISC itself was limiting.

To understand better the mechanism by which the 2′-O-methyloligonucleotide interacted with RISC, the concentration of free2′-O-methyl oligonucleotide required for half-maximal inhibition of RISCactivity (IC50; FIG. 2B-G) was measured at the six different RISCconcentrations determined in FIG. 2A. The IC50 for inhibition by free2′-O-methyl oligonucleotide is show for each RISC concentration in FIG.2H. The IC50 for the 2′-O-methyl oligonucleotide was remarkably close tohalf the RISC concentration. These data indicated that a single 31nucleotide 2′-O-methyl oligonucleotide bound each RISC and blocked itsfunction. Consistent with this apparent 1:1 stoichiometry, the data forthe 2 ′-O-methyl oligonucleotide titrations fit well to sigmoidal curveswith a Hill coefficient of 1 (FIG. 2B-G). The sequence specificity of2′-O-methyl oligonucleotide inhibition of RISC function clearly showsthat inhibition reflected binding of the oligo to the RISC. These dataare most easily explained if the concentration of the 2′-O-methyloligonucleotide required for inhibition in these experiments was muchgreater than the K_(D) for binding, i.e., the experiments were conductedin a stoichiometric binding regime. Under a stoichiometric bindingregime, inhibition by the 2′-O-methyl oligonucleotides would have beenessentially irreversible.

In theory, the 2′-O-methyl oligonucleotide may have acted by displacingthe passenger (sense) strand of the siRNA duplex, thereby blockingincorporation of the guide (anti-sense) strand into RISC (Elbashir etal., 2001c). This possibility can be excluded because a 5′ tethered 31nucleotide 2′-O-methyl oligonucleotide complementary to the passengerstrand of the siRNA did not deplete guide-strand RISC activity. (FIG.1B). Similarly, an anti-sense sequence 2′-O-methyl oligonucleotide couldnot pair with anti-sense RISC, but could pair with a sense target mRNA.This anti-sense 2′-O-methyl oligonucleotide was anticipated to pair withthe sense target mRNA and occlude the anti-sense RISC from the target.Surprisingly, this anti-sense 2′-O-methyl oligonucleotide was a poorinhibitor of anti-sense RISC function when it was used to bind thetarget site, requiring 300 nM for half-maximal inhibition in a reactioncontaining 14.5 nM RISC and 3 nM sense target RNA (FIG. 3A). Bycontrast, the same anti-sense 2′-O-methyl oligonucleotide was highlyeffective in blocking the activity of the sense RISC, to which it wascomplementary, acting with an IC50 of 8.2 nM in a reaction containing16.8 nM sense-strand RISC and 3 nM anti-sense target RNA (FIG. 3B). (Inthis experiment, sense-strand RISC was generated by changing the firstnucleotide of the sense-strand from C to U, thereby reversing thefunctional asymmetry (Schwarz et al., 2003).)

Thus, the interaction of 2′-O-methyl oligonucleotide with RISC wasdramatically different from the interaction of 2′-O-methyloligonucleotide with target RNA; RISC had a more than 40-fold greateraffinity for the 2′-O-methyl oligonucleotide than the oligonucleotidehad for the RNA target (compare FIGS. 2E and 3A). These data indicatedthat the interaction of RISC with target was not driven by simplenucleic acid hybridization. Inhibition of the siRNA-programmed RISC by a2′-O-methyl oligonucleotide with the sequence of the target RNA was moreeffective than inhibition mediated by binding of an oligonucleotide tothe target RNA itself. Thus, the RISC was more adept at finding and/orremaining bound to the target RNA than a 2′-O-methyl oligonucleotide.These data indicated that specific proteins in the RISC facilitatedeither target finding, target binding, or both. Consistent with thisidea, inhibition of RISC function was incomplete using 21 nucleotide2′-O-methyl oligonucleotides (data not shown). Thus, target sequenceflanking the site of complementarity to the siRNA guide strand likelyplays a role in target-RISC binding. An active mechanism that involvestarget sequences flanking the siRNA may facilitate the search for thetarget sequence.

Example 2 Inhibition of RNAi in Cultured Human Cells

The data presented in Example 1 showed that 2′-O-methyl oligonucleotideswere stoichiometric, irreversible, sequence-specific inhibitors of siRNAfunction in RNAi reactions using Drosophila embryo lysate. To addressthe question of whether 2′-O-methyl oligonucleotides could block siRNAfunction in vivo, sequential transfection experiments were performedusing 1, 5, 10 or 25 nM siRNA duplex. siRNA was transfected on the firstday, then reporter and control plasmids cotransfected together withvarious amounts of 2′-O-methyl oligonucleotide on the second day.Silencing of Pp-luc, relative to the Rr-luc control was measured on thethird day. For each siRNA concentration, the concentration of2′-O-methyl oligonucleotide required for half-maximal inhibition of RNAiwas determined (FIG. 4A-D). Increasing amounts of the 2′-O-methyloligonucleotide gradually extinguished the ability of the siRNA tosilence Pp-Luc in all four experiments. The inhibition of silencing inthe cultured cells could not have been a consequence of the 2′-O-methyloligonucleotide displacing the sense strand of the siRNA duplex, becauseassembly of siRNA into RISC occurred a full day before theoligonucleotide was introduced. When 10 nM siRNA was used in thetransfection, ˜1 nM 2′-O-methyl RNA was required for half-maximalinhibition of RNAi (FIG. 4C and E). At 25 nM siRNA, approximately 1.1 nM2′-O-methyl RNA was required to inhibit half the RNAi activity (FIG. 4Dand E). In FIG. 4E, siRNA concentration was plotted versus the amount of2′-O-methyl oligonucleotide required for half-maximal inhibition ofsilencing (IC50). The data fit well to a sigmoidal curve, consistentwith the idea that, at these concentrations, increasing amounts of siRNAdid not produce a corresponding increase in RISC activity. Higherconcentrations of siRNA could not be examined because they producedsequence-independent changes in gene expression (Persengiev et al.,2003; Semizarov et al., 2003). It was thus concluded that both cells andextracts had a limited capacity to assemble RISC on exogenous siRNA.These data indicated that the use of siRNA concentrations greater thanthat required to produce the maximum amount of RISC would lead to theaccumulation of double-stranded siRNA in vivo, and may thus contributeto undesirable, sequence non-specific responses sometimes observed incultured mammalian cells (Sledz et al., 2003).

Example 3 Inhibition of miRNA Function In Vitro and In Vivo

In animal cells, miRNAs are thought predominantly to function astranslational regulators. Nonetheless, a growing body of evidencesuggests that they function through a similar, if not identical, RISC assiRNAs (Hutvágner and Zamore, 2002; Zeng et al., 2002; Doench et al.,2003; Khvorova et al., 2003; Schwarz et al., 2003; Zeng et al., 2003b).Because 2′-O-methyl oligonucleotides blocked siRNA function in vitro andin cultured human cells, it was asked if these oligonucleotides mightlikewise disrupt the function of a specific miRNA in vitro and;in vivo.An ideal candidate for such an miRNA is let- 7. Classical geneticmutations in C. elegans let-7 produce well characterized, readily scoredphenotypes. Furthermore, human HeLa cells express multiple let-7 familymembers (Rfam Accession numbers MI0000060-MI0000068, MI0000433 andMI0000434), and endogenous let-7 is present naturally in RISC (Hutvágnerand Zamore, 2002; Zeng and Cullen, 2003). A 31 nucleotide 2′-O-methyloligonucleotide complementary to let-7 was tested for the ability toblock target cleavage guided by the endogenous let-7-programmed RISCpresent in HeLa S100 extract (FIG. 5A). (The assay detected thetarget-cleaving activity of let-7; endogenous human mRNA targets whosetranslation may be repressed by let-7 have not yet been tested.) As acontrol, the oligonucleotide was tested for the ability to block theactivity of a let-7-containing RISC assembled in vitro in Drosophilaembryo lysate. Addition of this 2′-O-methyl oligonucleotide efficientlyblocked target RNA cleavage directed by the endogenous let-7-programmedRISC in the HeLa S100 extract and by the RISC programmed with exogenouslet-7 siRNA duplex in Drosophila embryo lysate (FIG. 5C). In addition tocontaining endogenous let-7-programmed RISC, HeLa S100 can be programmedwith exogenous siRNA duplexes (Martinez et al., 2002; Schwarz et al.,2002). The target RNA used in FIG. 5B also contained sequence from thePp-luc mRNA, and could therefore be targeted by a Pp-luc-specific siRNAduplex (FIGS. 1A and 5C). The Pp-luc siRNA duplex was incubated with thehuman HeLa S100 extract to form Pp-luc-directed RISC.let-7-complementary 2′-O-methyl oligonucleotide and the target RNA werethen added. The oligonucleotide blocked cleavage by the endogenouslet-7-programmed RISC, but had no effect on cleavage directed by theexogenous Pp-luc siRNA in the same reaction (FIG. 5D). When tethered toa paramagnetic bead, this oligonucleotide could also quantitativelydeplete the let-7-programmed RISC from the Drosophila embryo lysate(FIG. SE), demonstrating that, again, the interaction between the2′-O-methyl oligonucleotide and the RISC was apparently irreversible.The 2′-O-methyl oligonucleotide was a specific and potent inhibitor oftarget cleavage directed by a naturally occurring, miRNA-programmedRISC. Furthermore, these data demonstrated that individual RISCcomplexes acted independently even when they targeted the same RNA.Next, 2′-O-methyl oligonucleotides were tested for the ability toinhibit miRNA function in vivo. Translational repression directed bymiRNAs occurs in C. elegans, where both the lin-4 and let-7 miRNAs havebeen shown to block translation of their target mRNAs without alteringmRNA stability (Wightman et al., 1993; Ha et al., 1996; Moss et al.,1997; Olsen and Ambros, 1999; Reinhart et al., 2000; Seggerson et al.,2002). The genetics of lin-4 and let-7 function are well characterizedin worms, where they are required during larval development to controlthe timing and pattern of cell division in the hypodermis (Lee et al.,1993; Reinhart et al., 2000). First, 2′-O-methyl oligonucleotidescomplementary to either lin-4 or let-7 were injected into the germlineof wild-type adult hermaphrodites to examine whether the RISCinactivators could block lin-4 or let-7 function during the larvaldevelopment of the resulting progeny. Although the 2′-O-methyloligonucleotides were not toxic, and when coinjected with an unrelatedDNA transformation reporter did not prevent the uptake and expression ofthe coinjected DNA, inhibition of lin-4 or let-7 activity was notobserved (data not shown). This finding indicated that single stranded2′-O-methyl oligonucleotides were not efficiently transmitted to theprogeny of injected animals. To circumvent this problem, 2′-O-methyloligonucleotides were injected directly into larvae and phenotypes ofthe injected animals were examined. The lin-4 miRNA functions in L1/L2larvae and the inventors have found that L1 larvae do not survivemicroinjection (data not shown), thus it was not possible to assay forinhibition of lin-4 function by direct injection. In contrast, let-7functions during the L4 stage, and L2 and L3 larvae were found tosurvive the microinjection procedure (See Experimental Procedures). Lossof let-7 function causes worms to reiterate the L4 larval molt andinappropriately produce larval cuticle at the adult stage.Loss-of-function let-7 phenotypes include weak cuticles prone tobursting at the vulva, defects in egg-laying, and loss of adult-specificcuticular structures that run the length of the animal's body, the alae(Reinhart et al., 2000). After larvae were injected with thelet-7-specific 2′-Omethyl oligonucleotide, 80% of the adult worms lackedalae; 77% lacked alae and also exhibited bursting vulvae (FIG. 6A). Incontrast, animals injected with an unrelated control 2′-O-methyloligonucleotide displayed no abnormal phenotypes (FIG. 6A). All of thephenotypes associated with injection of the let-7 complementary2′-O-methyl oligonucleotide were consistent with a loss of let-7activity. let-7 represses translation of lin-41 (Locus link ID 172760)mRNA by binding to a partially complementary site in the lin-41 3′untranslated region (Reinhart et al., 2000; Slack et al., 2000; Vella etal., 2004). Consequently, many of the phenotypes associated with theloss of let-7 reflect overexpression of LIN-41 protein; let-7 mutantsare partially suppressed by mutations in lin-41. It was reasoned that ifthe phenotypes observed in the injected larvae reflected a loss of let-7activity, then they should likely be partially suppressed by a lin-41mutation (Reinhart et al., 2000; Slack et al., 2000). To test thispossibility, the let-7-specific 2′-O-methyl oligonucleotide was injectedinto the lin-41(ma104) strain and penetrance of phenotypes was comparedwith an injected wild-type population. Consistent with the idea that theinjected oligonucleotide specifically inactivates let-7, the absence ofalae and vulval bursting phenotypes were both suppressed in thelin-41(ma104) mutant strain (FIG. 6A). The number of worms lacking alaewas reduced from 80% to 16%, and worms with bursting vulvae weredramatically reduced (74% in wild-type compared to 3.8%in lin-41(ma104)strain). The observed suppression (64%) was nearly identical to thatreported for a let-7, lin-41 genetic double mutant (70%; Reinhart etal., 2000; Slack et al., 2000). Together, these data support the idea2′-O-methyl oligonucleotides can act as potent inhibitors of miRNAfunction in vivo and can further be used to probe the function ofspecific miRNAs in vivo.

Example 4 Isolation of Protein-miRNA Complex Using a Tethered2′-O-Methyl Oligonucleotide

The in vitro experiments presented above indicated that both siRNA- andmiRNA-containing RISCs were stably bound by 2′-O-methyloligonucleotides. It was next tested whether tethered 2′-O-methyloligonucleotides could be used to isolate cellular factors associatedwith specific miRNAs. In human cells, miRNAs such as let-7 have beenidentified to occupy a protein complex that contains Argonaute proteins(Hutvágner and Zamore, 2002; Mourelatos et al., 2002; Dostie et al.,2003). In C. elegans, the Argonaute protein-encoding genes alg-1 andalg-2 were shown to be required for the biogenesis and/or function ofthe miRNAs lin-4 and let-7 (Grishok et al., 2001), but it was not shownif ALG-1 and ALG-2 proteins were directly associated with let-7.Extracts were prepared from wild-type adult worms carrying a transgeneexpressing GFP-tagged ALG-1 and ALG-2 proteins. The extracts were thenincubated with the let-7-complementary 2′-O-methyl oligonucleotidetethered by a 5′ biotin to streptavidin-conjugated paramagnetic beads.As a control, the experiment was performed in parallel using anoligonucleotide not complementary to let-7. The let-7 complementary, butnot the control, oligonucleotide depleted nearly all the let-7 miRNAfrom the extract (FIG. 6B). Western blotting using anti-GFP antibodyrevealed that both GFP-tagged ALG-1 and ALG-2 protein co-purified withthe let-7-complementary oligonucleotide, but not the controloligonucleotide (FIG. 6C). In contrast, the RNA binding protein, RDE4(Locus link ID176438), which is required for RNAi but not for miRNAfunction in C. elegans, did not co-purify with the let-7 complementarityoligonucleotide, providing further support for the specificity of thelet-7:ALG-1/ALG-2 interaction (FIG. 6C).

Finally, coimmunoprecipitation assay was employed to examine theinteraction between let-7 and ALG-1/ALG-2. In this assay, a monoclonalanti-GFP antibody was used to co-immunoprecipitate ALG-1/ALG-2 smallRNAs from the GFP::ALG-1/GFP::ALG-2 strain, which expressedGFP-ALG-1/ALG-2 fusion proteins (FIG. 6E). Northern analysis of theimmune complex showed that it contained mature 22 nucleotide let-7 miRNA(FIG. 6D). No detectable let-7 was recovered with the anti-GFP antibodyfrom the N2 wild-type strain. By comparing the fraction of let-7associated with GFP::ALG-1I/ALG-2 with the unbound fraction of let-7miRNA, it was estimated that approximately 30% of the 22 nucleotidelet-7 RNAs co-immunoprecipitated with GFP::ALG-1 and GFP::ALG-2. Thesedata support a model in which ALG-1 and ALG-2 form a complex, in vivo,that contains a substantial fraction of the mature let-7 miRNA.

Example 5 Identification of let-7-Regulated Transcripts

Use of 2′-O-methyl oligonucleotides designed to inhibit human let-7enabled identification and characterization of target genes and pathwayswhich are regulated by the human let-7 miRNA family. An experimentalsystem was developed based on two human cell lines. HeLa cells exhibitedhigh levels of let-7 expression and presented an ideal subject for let-7inhibition studies, whereas undifferentiated NT2 cells did not expressthe let-7 gene family and presented a cell type in which let-7 could betransiently “over-expressed” by transfecting it as an siRNA into thecells (FIG. 7A). Inhibition and over-expression of let-7 were monitoredin these respective cell types using a sensor target plasmid containinga let-7 complementary site, which controls luciferase expression.Inhibition of let-7 in HeLa cells produced a several-fold increase inluciferase expression, while expression of let-7 in NT2 cells resultedin a several-fold decrease in luciferase expression (FIG. 7B, C, D).

Human gene expression profiles were assessed for both let-7inhibitor-treated and untreated HeLa cells, and for let-7 treated NT2cells using microarrays. mRNAs whose expression was reduced in the let-7expressing cells (NT2 cells) and/or induced in the let-7 suppressedcells (HeLa cells) were identified. Two genes, HMGA2 and Dicer, wereboth significantly induced in HeLa cells upon let-7 inhibition using2′-O-methyl oligonucleotides and were significantly repressed in NT2cells as a consequence of let-7 transfection. Additionally, severalgenes were identified in which expression was affected by inhibition orinduction of let-7 (FIG. 8A). Many of these mRNAs, including HMGA2 andDicer, contain predicted multiple let-7 recognition elements. For HMGA2and Dicer, the microarray data were confirmed for transcript and proteinexpression effects using real-time PCR and western blot analysis (FIG.8B, C; FIG. 9).

These data demonstrate the powerful, effective use of 2′-O-methyloligonucleotides to identify miRNA targets through direct,sequence-specific inhibition of miRNA function. Transiently expressedmiRNA (transfected as an siRNA) was also demonstrated to regulate itsnatural target mRNAs. Further, it has now been shown that induction orinhibition of a miRNA produced significant changes in the expression ofthe target mRNA, which could be readily scored using expressionprofiling.

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Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

1. A method for inhibiting RNA silencing of a gene, comprising,contacting a cell or organism containing an siRNA or miRNA that directsRNA silencing of a gene, with a RISC inactivator, such that RNAsilencing of a gene is inhibited.
 2. (canceled)
 3. A method fordetecting siRNA or miRNA-associated factors, comprising, contacting acell or composition comprising of a siRNA or miRNA that directs RNAsilencing of a gene, with a RISC inactivator, and enriching for the RISCinactivator, siRNA or miRNA and any associated factors, such that siRNAor miRNA-associated factors are detected.
 4. The method of claim 1,wherein the RISC inactivator is nuclease-resistant.
 5. The method ofclaim 1, wherein the RISC inactivator is ribonuclease-resistant.
 6. Themethod of claim 1, wherein the RISC inactivator is a 2′-O-methyloligonucleotide.
 7. The method of claim 1, wherein the oligonucleotidemodification is selected from the group consisting of the 2′-OH groupreplaced by a H, alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR,NR2,), or CN group, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.8. The method of claim 1, wherein the cell or organism is a Drosophilamelanogaster cell or organism.
 9. The method of claim 8, wherein thecell or organism is a Drosophila melanogaster embryo.
 10. The method ofclaim 1, wherein the cell or organism is a C. elegans cell or organism.11. The method of claim 1, wherein the cell or organism is a mammaliancell or organism. 12-13. (canceled)
 14. The method of claim 3, whereinthe RISC inactivator is nuclease-resistant.
 15. The method of claim 3,wherein the RISC inactivator is ribonuclease-resistant.
 16. The methodof claim 3, wherein the RISC inactivator is a 2′-O-methyloligonucleotide.
 17. The method of claim 3, wherein the oligonucleotidemodification is selected from the group consisting of the 2′-OH groupreplaced by a H, alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR,NR2,), or CN group, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.18. The method of claim 3, wherein the composition is a cell extract.19. The method of claim 3, wherein the composition is a Drosophilamelanogaster cell extract.
 20. The method of claim 19, wherein thecomposition is a Drosophila melanogaster embryo cell extract.
 21. Themethod of claim 3, wherein the composition is a C. elegans cell extract.22. The method of claim 3, wherein the composition is a mammalian cellextract.
 23. A method for detecting factors associated with a RISCinactivator, comprising, attaching a RISC inactivator to a surface, andcontacting the RISC inactivator with a composition comprising an siRNAor miRNA that directs RNA silencing of a gene, such that factorsassociated with the RISC inactivator are detected.
 24. The method ofclaim 23, wherein the RISC inactivator is nuclease-resistant.
 25. Themethod of claim 23, wherein the RISC inactivator isribonuclease-resistant.
 26. The method of any of claim 23, wherein theRISC inactivator is a 2′-O-methyl oligonucleotide.
 27. The method ofclaim 23, wherein the oligonucleotide modification is selected from thegroup consisting of the 2′-OH group replaced by a H, alkoxy or OR,halogen, SH, SR, amino (such as NH2, NHR, NR2,), or CN group, wherein Ris lower alkyl, alkenyl, alkynyl, or aryl.
 28. The method of claim 23,wherein the surface is a bead.
 29. The method of claim 28, wherein theRISC inactivator is tethered to a streptavidin bead via a 5′ biotinlinkage. 30-31. (canceled)
 32. The method of claim 23, wherein thecomposition is a cell extract comprising an siRNA or miRNA.
 33. A methodfor identifying active miRNAs, comprising, contacting a series or arraycomprising RISC inactivators, wherein the series or array is enrichedfor RISC inactivators, as compared to random or extant arrays or seriesof oligonucleotide, genomic, EST, or mRNA sequences, with a cell extractcomprising miRNAs, and detecting association of cell extract miRNAs withRISC inactivators, such that active miRNAs are identified. 34-44.(canceled)
 45. A method for monitoring sequence-specific inhibition ofRNA silencing, comprising, contacting a cell, cell extract or organismcomprising of a reporter RNA and containing an siRNA or miRNAsufficiently complementary to the reporter RNA, with a RISC inactivator,and detecting the cleavage state of the reporter RNA, such thatinhibition of RNA silencing is monitored. 46-47. (canceled)
 48. A methodfor monitoring sequence-specific inhibition of RNA silencing,comprising, contacting a cell, cell extract or organism comprising of areporter RNA and containing an siRNA or miRNA sufficiently complementaryto the reporter RNA, with a RISC inactivator, and detecting theexpression level or activity of the polypeptide encoded by the reporterRNA, such that inhibition of RNA silencing is monitored. 49-50.(canceled)
 51. The method of claim 45 or 48, wherein the RISCinactivator is nuclease-resistant.
 52. The method of claim 45 or 48,wherein the RISC inactivator is ribonuclease-resistant.
 53. The methodof claim 45 or 48, wherein the RISC inactivator is a 2′-O-methyloligonucleotide.
 54. The method of claim 45 or 48, wherein theoligonucleotide modification is selected from the group consisting ofthe 2′-OH group replaced by a H, alkoxy or OR, halogen, SH, SR, amino(such as NH2, NHR, NR2,), or CN group, wherein R is lower alkyl,alkenyl, alkynyl, or aryl.
 55. The method of claim 45 or 48, wherein thecell, cell extract or organism is a Drosophila melanogaster cell, cellextract or organism.
 56. The method of claim 45 or 48, wherein the cell,cell extract or organism is a C. elegans cell, cell extract or organism.57. The method of claim 45 or 48, wherein the cell, cell extract ororganism is a mammalian cell, cell extract or organism.
 58. The methodof claim 45 or 48, wherein the reporter RNA is radioactively labeled.59. The method of claim 45 or 48, wherein the reporter RNA isfluorescently labeled.
 60. A method for identifying a compound thatmodulates the interaction of a RISC inactivator with a miRNA or siRNA,comprising, contacting a composition, cell, cell extract or organismcomprising: (1) a reporter RNA (2) a miRNA or siRNA sufficientlycomplementary to the reporter RNA, and (3) a RISC inactivator, with atest compound, and detecting the cleavage state of the reporter RNA, orthe expression level or activity of the polypeptide encoded by thereporter RNA, such that a compound that modulates the interaction of aRISC inactivator with a miRNA or siRNA is identified. 61-62. (canceled)63. The method of claim 60, wherein the compound is selected from thegroup consisting of a small molecule, a peptide, a polynucleotide, anantibody or biologically active portion thereof, a peptidomimetic, and anon-peptide oligomer.
 64. The method of claim 60, wherein the RISCinactivator is nuclease-resistant.
 65. The method of claim 60, whereinthe RISC inactivator is ribonuclease-resistant.
 66. The method of claim60, wherein the RISC inactivator is a 2′-O-methyl oligonucleotide. 67.The method of claim 60, wherein the oligonucleotide modification isselected from the group consisting of the 2′-OH group replaced by a H,alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR, NR2,), or CNgroup, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.
 68. Themethod of claim 60, wherein the cell, cell extract or organism is aDrosophila melanogaster cell, cell extract or organism.
 69. The methodof claim 60, wherein the cell, cell extract or organism is a C. eleganscell, cell extract or organism.
 70. The method of claim 60, wherein thecell, cell extract or organism is a mammalian cell, cell extract ororganism.
 71. The method of claim 60, wherein the reporter RNA isradioactively labeled.
 72. The method of claim 60, wherein the reporterRNA is fluorescently labeled.
 73. A method for identifying a compoundthat modulates the interaction of a factor associated with a (miRNA-RISCinactivator) complex or a (siRNA-RISC inactivator complex), comprising,contacting a composition comprising a miRNA or a siRNA, and a RISCinactivator, with a test compound, and enriching for the RISCinactivator, miRNA or siRNA, and any associated factors, such that acompound that modulates the interaction of a factor associated with the(miRNA-RISC inactivator) complex or a (siRNA-RISC inactivator) complexis identified.
 74. (canceled)
 75. The method of claim 73, wherein thecompound is selected from the group consisting of a small molecule, apeptide, a polynucleotide, an antibody or biologically active portionthereof, a peptidomimetic, and a non-peptide oligomer.
 76. The method ofclaim 73, wherein the RISC inactivator is nuclease-resistant.
 77. Themethod of claim 73, wherein the RISC inactivator isribonuclease-resistant.
 78. The method of claim 73, wherein the RISCinactivator is a 2′-O-methyl oligonucleotide.
 79. The method of claim73, wherein the oligonucleotide modification is selected from the groupconsisting of the 2′-OH group replaced by a H, alkoxy or OR, halogen,SH, SR, amino (such as NH2, NHR, NR2,), or CN group, wherein R is loweralkyl, alkenyl, alkynyl, or aryl.
 80. The method of claim 73, whereinthe levels or identities of factors associated with the miRNA-RISCinactivator complex are compared to an appropriate control.
 81. Themethod of claim 73, wherein the levels or identities of factorsassociated with the miRNA-RISC inactivator complex are compared withlevels or identities of factors associated with the miRNA-RISCinactivator complex in the absence of compound.
 82. A method formeasuring the level of programmed RISC for a gene, comprising, attachinga RISC inactivator to a surface, and contacting the RISC inactivatorwith a composition comprising a labeled siRNA or miRNA that directs RNAsilencing of a gene, such that the level of programmed RISC for a geneis detected.
 83. The method of claim 82, wherein the siRNA or miRNA isradioactively labeled.
 84. The method of claim 82, wherein the siRNA ormiRNA is fluorescently labeled.
 85. The method of claim 82, wherein theRISC inactivator is nuclease-resistant.
 86. The method of claim 82,wherein the RISC inactivator is ribonuclease-resistant.
 87. The methodof claim 82, wherein the RISC inactivator is a 2′-O-methyloligonucleotide.
 88. The method of claim 82, wherein the oligonucleotidemodification is selected from the group consisting of the 2′-OH groupreplaced by a H, alkoxy or OR, halogen, SH, SR, amino (such as NH2, NHR,NR2,), or CN group, wherein R is lower alkyl, alkenyl, alkynyl, or aryl.89. The method of claim 82, wherein the surface is a bead.
 90. Themethod of claim 89, wherein the RISC inactivator is tethered to astreptavidin bead via a 5′ biotin linkage. 91-92. (canceled)
 93. Themethod of claim 82, wherein the composition is a cell extract comprisingan siRNA or miRNA.
 94. A 2′-0-methyl oligonucleotide RISC inactivator.95-97. (canceled)
 98. The RISC inactivator of claim 94, wherein theoligonucleotide modification is selected from the group consisting ofthe 2′-OH group replaced by a H, alkoxy or OR, halogen, SH, SR, amino(such as NH2, NHRS, NR2,), or CN group, wherein R is lower alkyl,alkenyl, alkynyl, or aryl.
 99. A composition comprising the RISCinactivator of claim 94 and a pharmaceutically acceptable carrier.100-118. (canceled)
 119. A method for inhibiting HMGA2 expressioncomprising contacting a cell with a let-7 polynucleotide or fragmentthereof, such that HMGA2 expression is inhibited.
 120. A method forenhancing HMGA2 expression comprising contacting a cell that containslet-7 or a fragment thereof with a let-7-RISC inactivator, such thatHMGA2 expression is enhanced.
 121. A method for inhibiting Dicerexpression comprising contacting a cell with a let-7 polynucleotide orfragment thereof, such that Dicer expression is inhibited.
 122. A methodfor enhancing Dicer expression comprising contacting a cell thatcontains let-7 or a fragment thereof with a let-7-RISC inactivator, suchthat Dicer expression is enhanced.
 123. A method for identifying acompound that modulates the interaction of let-7-RISC with a Dicertranscript, comprising, contacting a cell containing let-7-RISC, with atest compound, and determining the expression level and/or activity ofDicer, such that a compound that modulates the interaction of let-7-RISCwith Dicer transcript is identified.
 124. A method for identifying RNAsmodulated by an RNA silencing agent comprising, contacting a cell thatcontains an RNA silencing agent with a RISC inactivator; comparing theRNA expression levels of the RISC inactivator-contacted cell with theRNA expression levels of a cell that is not contacted with the RISCinactivator; and identifying RNAs whose expression level is modulated bytreatment with the RISC inactivator, such that RNAs modulated by the RNAsilencing agent are identified.
 125. A method for identifyingpolypeptides whose expression is modulated by an RNA silencing agentcomprising, contacting a cell that contains an RNA silencing agent witha RISC inactivator; comparing the polypeptide expression levels of theRISC inactivator-contacted cell with the polypeptide expression levelsof a cell that is not contacted with the RISC inactivator; andidentifying polypeptides whose expression level is modulated bytreatment with the RISC inactivator, such that polypeptides whoseexpression is modulated by the RNA silencing agent are identified.